%
%   Papers that we reference, BUT NOT any paper that uses PETSc or is about PETSc
% those belong in petscapp.bib
%
%   DO NOT DEFINE ANY ABREVIATIONS TO USE IN ENTRIES BELOW: Always write out the names of journels etc
@article{dunning2017jump,
  title={{JuMP}: a modeling language for mathematical optimization},
  author={Dunning, Iain and Huchette, Joey and Lubin, Miles},
  journal={SIAM Review},
  volume={59},
  number={2},
  pages={295--320},
  year={2017},
  publisher={SIAM}
}
@inproceedings{PrudencioSchulz2011,
  title     = {The parallel {C++} statistical library {QUESO}: Quantification of Uncertainty for Estimation, Simulation and Optimization},
  author    = {Ernesto E Prudencio and Karl W Schulz},
  booktitle = {European Conference on Parallel Processing},
  pages     = {398--407},
  year      = {2011},
}
@Misc{rol-website,
  key          = {ROL},
  title        = {{Rapid Optimization Library} Website},
  howpublished = {\url{https://trilinos.org/packages/rol}},
  year         = {2018}
}
@article{more1994line,
  title={Line search algorithms with guaranteed sufficient decrease},
  author={Mor{\'e}, Jorge J and Thuente, David J},
  journal={ACM Transactions on Mathematical Software},
  volume={20},
  number={3},
  pages={286--307},
  year={1994},
  publisher={ACM}
}
@article{griewank2000algorithm,
  title={Algorithm 799: revolve: an implementation of checkpointing for the reverse or adjoint mode of computational differentiation},
  author={Griewank, Andreas and Walther, Andrea},
  journal={ACM Transactions on Mathematical Software},
  volume={26},
  number={1},
  pages={19--45},
  year={2000},
  publisher={ACM}
}

@article{metcalf2011seven,
  title={The seven ages of fortran},
  author={Metcalf, Michael},
  journal={Journal of Computer Science \& Technology},
  volume={11},
  year={2011}
}

@Article{Giraldo_2013,
  Title                    = {Implicit-explicit formulations of a three-dimensional nonhydrostatic unified model of the atmosphere {(NUMA)}},
  Author                   = {F.X. Giraldo and J.F. Kelly and E.M. Constantinescu},
  Journal                  = {SIAM Journal on Scientific Computing},
  Year                     = {2013},
  Number                   = {5},
  Pages                    = {B1162-B1194},
  Volume                   = {35},

  Doi                      = {10.1137/120876034}
}

@ARTICLE{Constantinescu_TR2016b,
   author = {Constantinescu, E.M.},
    title = {Estimating Global Errors in Time Stepping},
  journal = {ArXiv e-prints},
archivePrefix = "arXiv",
   eprint = {1503.05166},
 primaryClass = "math.NA",
 keywords = {Mathematics - Numerical Analysis, 65L05, 65L06, 65L20, 65L70},
     year = 2016,
    month = mar,
   adsurl = {http://adsabs.harvard.edu/abs/2015arXiv150305166C},
  adsnote = {Provided by the SAO/NASA Astrophysics Data System}
}


@Article{Pareschi_2005,
  Title                    = {Implicit-Explicit {R}unge-{K}utta Schemes and Applications to Hyperbolic Systems with Relaxation},
  Author                   = {L. Pareschi and G. Russo},
  Journal                  = {Journal of Scientific Computing},
  Year                     = {2005},
  Number                   = {1},
  Pages                    = {129--155},
  Volume                   = {25}
}

@Article{Kennedy_2003,
  Title                    = {Additive {R}unge-{K}utta schemes for convection-diffusion-reaction equations},
  Author                   = {C.A. Kennedy and M.H. Carpenter},
  Journal                  = {Appl. Numer. Math.},
  Year                     = {2003},
  Number                   = {1-2},
  Pages                    = {139--181},
  Volume                   = {44},

  Doi                      = {10.1016/S0168-9274(02)00138-1},
  Publisher                = {Elsevier Science Publishers B. V.}
}

@Unpublished{Boscarino_TR2011,
  Title                    = {Implicit-Explicit {R}unge-{K}utta schemes for hyperbolic systems and kinetic equations in the diffusion limit},
  Author                   = {Boscarino, S. and Pareschi, L. and Russo, G.},
  Note                     = {Arxiv preprint arXiv:1110.4375},
  Year                     = {2011}
}

@Article{Ascher_1997,
  Title                    = {Implicit-explicit {R}unge-{K}utta methods for time-dependent partial differential equations},
  Author                   = {U.M. Ascher and S.J. Ruuth and R.J. Spiteri},
  Journal                  = {Applied Numerical Mathematics},
  Year                     = {1997},
  Pages                    = {151--167},
  Volume                   = {25}
}

@Article{Sandu_1997,
  Title                    = {Benchmarking stiff ode solvers for atmospheric chemistry problems {II}: {R}osenbrock solvers},
  Author                   = {A. Sandu and J.G. Verwer and J.G. Blom and E.J. Spee and G.R. Carmichael and F.A. Potra},
  Journal                  = {Atmospheric Environment},
  Year                     = {1997},
  Number                   = {20},
  Pages                    = {3459--3472},
  Volume                   = {31},

  Abstract                 = {In the numerical simulation of atmospheric transport-chemistry processes, a major task is the integration of the stiff systems of ordinary differential equations describing the chemical transformations. It is therefore of interest to systematically search for stiff solvers which can be identified as close to optimal for atmospheric applications. In this paper we continue our investigation from Sandu et al. (1996, CWI Report NM-R9603 and Report in Comput. Math., No. 85) and compare eight solvers on a set of seven box-models used in present day models. The focus is on Rosenbrock solvers. These turn out to be very well suited for our application when they are provided with highly efficient sparse matrix techniques to economize on the linear algebra. Two of the Rosenbrock solvers tested are from the literature, viz. and 4, and two are new and specially developed for air quality applications, viz. 3 and 3. }
}

@Article{Rang_2005,
  Title                    = {New {R}osenbrock {W}-methods of order 3 for partial differential algebraic equations of index 1},
  Author                   = {Rang, J. and Angermann, L.},
  Journal                  = {BIT Numerical Mathematics},
  Year                     = {2005},
  Number                   = {4},
  Pages                    = {761--787},
  Volume                   = {45},
  Publisher                = {Springer}
}

@article{GottliebKetchesonShu2009,
  author  = {Sigal Gottlieb and David I. Ketcheson and Chi Wang Shu},
  title   = {{High order strong stability preserving time discretizations}},
  journal = {Journal of Scientific Computing},
  volume  = {38},
  number  = {3},
  pages   = {251--289},
  doi     = {10.1007/s10915-008-9239-z},
  year    = {2009}
}
@Article{Ketcheson_2008,
  Title                    = {Highly Efficient Strong Stability-Preserving {R}unge--{K}utta Methods with Low-Storage Implementations},
  Author                   = {D.I. Ketcheson},
  Journal                  = {SIAM Journal on Scientific Computing},
  Year                     = {2008},
  Number                   = {4},
  Pages                    = {2113--2136},
  Volume                   = {30},

  Doi                      = {10.1137/07070485X},
  Keywords                 = {method of lines, strong stability-preserving, monotonicity, low-storage, RungeKutta methods},
  Publisher                = {SIAM}
}

@Article{Jansen_2000,
  Title                    = {A generalized-$\alpha$ method for integrating the filtered {N}avier--{S}tokes equations with a stabilized finite element method},
  Author                   = {Jansen, K.E. and Whiting, C.H. and Hulbert, G.M.},
  Journal                  = {Computer Methods in Applied Mechanics and Engineering},
  Year                     = {2000},
  Number                   = {3},
  Pages                    = {305--319},
  Volume                   = {190},

  Publisher                = {Elsevier}
}

@Article{Butcher_2007,
  Title                    = {Error propagation of general linear methods for ordinary differential equations},
  Author                   = {J.C. Butcher and Z. Jackiewicz and W.M. Wright},
  Journal                  = {Journal of Complexity},
  Year                     = {2007},
  Number                   = {4-6},
  Pages                    = {560--580},
  Volume                   = {23},

  Abstract                 = {We discuss error propagation for general linear methods for ordinary differential equations up to terms of order p+2, where p is the order of the method. These results are then applied to the estimation of local discretization errors for methods of order p and for the adjacent order p+1. The results of numerical experiments confirm the reliability of these estimates. This research has applications in the design of robust stepsize and order changing strategies for algorithms based on general linear methods.},
  Doi                      = {10.1016/j.jco.2007.01.009},
  ISSN                     = {0885-064X}
}

@Article{Constantinescu_A2010a,
  Title                    = {Extrapolated implicit-explicit time stepping},
  Author                   = {E.M. Constantinescu and A. Sandu},
  Journal                  = {SIAM Journal on Scientific Computing},
  Year                     = {2010},
  Number                   = {6},
  Pages                    = {4452-4477},
  Volume                   = {31},

  Comment                  = {Preprint \# ANL/MCS-P1612-0409},
  Doi                      = {10.1137/080732833}
}


@inproceedings{devito2011liszt,
  title={Liszt: a domain specific language for building portable mesh-based PDE solvers},
  author={DeVito, Zachary and Joubert, Niels and Palacios, Francisco and Oakley, Stephen and Medina, Montserrat and Barrientos, Mike and Elsen, Erich and Ham, Frank and Aiken, Alex and Duraisamy, Karthik and others},
  booktitle={Proceedings of 2011 International Conference for High Performance Computing, Networking, Storage and Analysis},
  pages={9},
  year={2011},
  organization={ACM}
}

@article{devito2011designing,
  title={Designing the Language Liszt for Building Portable Mesh-based PDE Solvers},
  author={DeVito, Zachary and Hanrahan, Pat},
  journal={Scientific Discovery through Advanced Computing Program (SciDAC)},
  year={2011}
}

@Misc{PGASintro,
  author = {Tim Stitt},
  title  = {An Introduction to the Partitioned Global Address Space (PGAS) Programming Model},
  note   = {\url{http://cnx.org/content/m20649/latest/}}
}

@inproceedings{el2006upc,
  title={UPC: unified parallel C},
  author={El-Ghazawi, Tarek and Smith, Lauren},
  booktitle={Proceedings of the 2006 ACM/IEEE conference on Supercomputing},
  pages={27},
  year={2006},
  organization={ACM}
}

@inproceedings{numrich1998co,
  title={Co-Array Fortran for parallel programming},
  author={Numrich, Robert W and Reid, John},
  booktitle={ACM Sigplan Fortran Forum},
  volume={17},
  number={2},
  pages={1--31},
  year={1998},
  organization={ACM}
}

@article{aiken1997titanium,
  title={Titanium: A high-performance Java dialect},
  author={Aiken, Alex and Colella, Phil and Gay, David and Graham, Susan and Hilfinger, Paul and Krishnamurthy, Arvind and Liblit, Ben and Miyamoto, Carleton and Pike, Geoff and Semenzato, Luigi and others},
  year={1997}
}

@article{charles2005x10,
  title={X10: an object-oriented approach to non-uniform cluster computing},
  author={Charles, Philippe and Grothoff, Christian and Saraswat, Vijay and Donawa, Christopher and Kielstra, Allan and Ebcioglu, Kemal and Von Praun, Christoph and Sarkar, Vivek},
  journal={Acm Sigplan Notices},
  volume={40},
  number={10},
  pages={519--538},
  year={2005},
  publisher={ACM}
}

@article{chamberlain2007parallel,
  title={Parallel programmability and the chapel language},
  author={Chamberlain, Bradford L and Callahan, David and Zima, Hans P},
  journal={International Journal of High Performance Computing Applications},
  volume={21},
  number={3},
  pages={291--312},
  year={2007},
  publisher={SAGE Publications}
}

@inproceedings{CharmppOOPSLA93,
  author        = "{Kal\'{e}}, L.V. and Krishnan, S.",
  title         = "{CHARM++: A Portable Concurrent Object Oriented System
                   Based on C++}",
  editor        = "Paepcke, A.",
  fulleditor    = "Paepcke, Andreas",
  pages         = "91--108",
  Month         = "September",
  Year          = "1993",
  booktitle     = "{Proceedings of OOPSLA'93}",
  publisher     = "{ACM Press}",
}

@inproceedings{hewitt1973universal,
  title={A universal modular actor formalism for artificial intelligence},
  author={Hewitt, Carl and Bishop, Peter and Steiger, Richard},
  booktitle={Proceedings of the 3rd international joint conference on Artificial intelligence},
  pages={235--245},
  year={1973},
  organization={Morgan Kaufmann Publishers Inc.}
}

@book{yonezawa1990abcl,
  title={ABCL: an object-oriented concurrent system},
  author={Yonezawa, Akinori},
  year={1990},
  publisher={MIT press}
}

@inproceedings{dally1988object,
  title={Object-oriented concurrent programming in CST},
  author={Dally, William J and Chien, Andrew A},
  booktitle={Proceedings of the third conference on Hypercube concurrent computers and applications: Architecture, software, computer systems, and general issues-Volume 1},
  pages={434--439},
  year={1988},
  organization={ACM}
}

@article{grimshaw1993easy,
  title={Easy-to-use object-oriented parallel processing with Mentat},
  author={Grimshaw, Andrew S.},
  journal={Computer},
  volume={26},
  number={5},
  pages={39--51},
  year={1993},
  publisher={IEEE}
}

@inproceedings{gannon1991object,
  title={Object oriented parallelism: pC++ ideas and experiments},
  author={Gannon, Dennis and Lee, JK},
  booktitle={Proceedings of},
  pages={13--23},
  year={1991}
}

@inproceedings{lau1992object,
  title={An object-oriented class library for scalable parallel heuristic search},
  author={Lau, Wing-cheong and Singh, Vineet},
  booktitle={ECOOP’92 European Conference on Object-Oriented Programming},
  pages={252--267},
  year={1992},
  organization={Springer}
}

@book{chase1989amber,
  title={The Amber system: Parallel programming on a network of multiprocessors},
  author={Chase, Jeffery and Amador, Franz and Lazowska, Edward and Levy, Henry and Littlefield, Richard},
  volume={23},
  number={5},
  year={1989},
  publisher={ACM}
}

@inproceedings{kaiser2009parallex,
  title={Parallex an advanced parallel execution model for scaling-impaired applications},
  author={Kaiser, Hartmut and Brodowicz, Maciej and Sterling, Thomas},
  booktitle={Parallel Processing Workshops, 2009. ICPPW'09. International Conference on},
  pages={394--401},
  year={2009},
  organization={IEEE}
}

@TechReport{ipm,
    Author = "Barry F. Smith",
    Title  = "A New Parallel Programming Model for Computer Simulation",
    Institution = "Argonne National Laboratory",
    Year   = 2014,
    Number = {ANL/MCS-P5135-0414}
    }

@article{groppsnir,
author = {William Gropp and Marc Snir},
title = {Programming for Exascale Computers},
journal ={Computing in Science and Engineering},
volume = {15},
number = {6},
issn = {1521-9615},
year = {2013},
pages = {27-35},
doi = {http://doi.ieeecomputersociety.org/10.1109/MCSE.2013.96},
publisher = {IEEE Computer Society},
address = {Los Alamitos, CA},
}

@book{mpi3,
  title="MPI: A Message-Passing Interface Standard, Version 3.0",
  author={Message Passing Interface Forum},
  year={2012},
  publisher={High Performance Computing Center Stuttgart (HLRS)}
}

@book{openmp4,
  title="OpenMP Application Program Interface, Version 4.0",
  year={2013},
  publisher={OpenMP Architecture Review Board}
}


@inproceedings{hartono2009annotation,
  title={Annotation-based empirical performance tuning using {Orio}},
  author={Hartono, Albert and Norris, Boyana and Sadayappan, Ponnuswamy},
  booktitle={Parallel \& Distributed Processing, 2009. IPDPS 2009. IEEE International Symposium on},
  pages={1--11},
  year={2009},
  organization={IEEE}
}

@book{toselli2005domain,
  title="Domain Decomposition Methods: Algorithms and Theory",
  author={Toselli, Andrea and Widlund, Olof B},
  volume={34},
  year={2005},
  publisher={Springer}
}

@inbook{st2016,
  author = "Barry F. Smith and Xumin Tu",
  chapter = "Domain Decomposition",
  title = "Encyclopedia of Applied and Computational Mathematics",
  bookeditor = "B. Engquist",
  publisher = "Springer",
  pages={375--381},
  year = "2016"
}

@TechReport{ saws,
    Author = "Matt Otten and Jed Brown and Barry F. Smith",
    Title  = "Scientific Application Web Server {(SAWs)} Users Manual",
    Institution = "Argonne National Laboratory",
    Year   = 2013
    }

@article{smith1997domain,
  title={Domain Decomposition Methods for Partial Differential Equations},
  author={Smith, B.F.},
  journal={ICASE LARC Interdisciplinary Series in Science and Engineering},
  volume={4},
  pages={225--244},
  year={1997},
  publisher={Citeseer}
}
@article{spillane2011abstract,
  title={Abstract robust coarse spaces for systems of {PDEs} via generalized eigenproblems in the overlaps},
  author={Spillane, N and Dolean, V and Hauret, P and Nataf, F and Pechstein, C and Scheichl, R},
  journal={NuMa-Report},
  volume={7},
  pages={2007},
  year={2011}
}

@inproceedings{jolivet2013scalabledd,
  title={Scalable domain decomposition preconditioners for heterogeneous elliptic problems},
  author={Jolivet, Pierre and Hecht, Fr{\'e}d{\'e}ric and Nataf, Fr{\'e}d{\'e}ric and Prud'homme, Christophe},
  booktitle={Proceedings of SC13: International Conference for High Performance Computing, Networking, Storage and Analysis},
  pages={80},
  year={2013},
  organization={ACM}
}

@book{KS2000,
	Author = {D. Kinderlehrer and G. Stampacchia},
	Publisher = {Society for Industrial Mathematics},
	Title = {An Introduction to Variational Inequalities and Their Applications},
	Year = {2000}
}
@article{wan2000energy,
  title={An energy-minimizing interpolation for robust multigrid methods},
  author={Wan, W.L. and Chan, T.F. and Smith, B. F.},
  journal={SIAM Journal on Scientific Computing},
  volume={21},
  number={4},
  pages={1632--1649},
  year={2000},
  publisher={Philadelphia, PA: SIAM, c1993-}
}

@article{chansmith1994,
  title={Domain decomposition and multigrid algorithms for elliptic problems on unstructured meshes},
  author={Chan, T.F. and Smith, B.F.},
  journal={Electronic Transactions on Numerical Analysis},
  volume={2},
  pages={171--182},
  year={1994}
}
@TechReport( proto-fsp,
    Author = "Venkatramani Balaji and Barry Smith and Brian Van Straalen and Priya Vashishta and  Michael Zarnstorff and Michael Zika",
    Title  = "Report of the {Proto-FSP} {Assessment Panel for the FSP}",
    Institution = "Princeton Plasma Physics Laboratory",
    Year   = 2010,
    url = {http://www.pppl.gov/fsp/documents/Proto-FSPAssessmentReport.pdf}
    )

@article{ipsen2001,
	Author = {Ilse C. F. Ipsen},
	Journal = {SIAM J. Sci. Comput.},
	Pages = {1050--1051},
        Volume = 23,
	Publisher = {SIAM},
	Title = {A Note on Preconditioning Nonsymmetric Matrices},
	Year = {2001}}
% Random papers on solvers for GPUs
@inproceedings{gpus-suck,
 author = {Vuduc, R. and Chandramowlishwaran, A. and Choi, J. and Guney M. },
 title = { On the Limits of {GPU} Acceleration},
 booktitle = {HOTPAR: Proceedings of the 2nd USENIX Workshop on Hot Topics in Parallelism},
 year = {2010},
 publisher = {USENIX}
 }
@inproceedings{882364,
 author = {Bolz, Jeff and Farmer, Ian and Grinspun, Eitan and Schr\"{o}oder, Peter},
 title = {Sparse matrix solvers on the {GPU}: conjugate gradients and multigrid},
 booktitle = {SIGGRAPH '03: ACM SIGGRAPH 2003 Papers},
 year = {2003},
 isbn = {1-58113-709-5},
 pages = {917--924},
 location = {San Diego, California},
 doi = {http://doi.acm.org/10.1145/1201775.882364},
 publisher = {ACM},
 address = {New York, NY},
 }
@conference{feng2008multigrid,
	Author = {Feng, Z. and Li, P.},
	Booktitle = {IEEE/ACM International Conference on Computer-Aided Design, 2008. ICCAD 2008},
	Date-Added = {2010-08-19 15:57:06 -0500},
	Date-Modified = {2010-08-19 15:57:06 -0500},
	Pages = {647--654},
	Title = {Multigrid on {GPU}: Tackling power grid analysis on parallel SIMT platforms},
	Year = {2008}}

@conference{goodnight2003multigrid,
	Author = {Goodnight, N. and Woolley, C. and Lewin, G. and Luebke, D. and Humphreys, G.},
	Booktitle = {Proceedings of the ACM SIGGRAPH/EUROGRAPHICS conference on Graphics hardware},
	Date-Added = {2010-08-19 15:45:20 -0500},
	Date-Modified = {2010-08-19 15:45:20 -0500},
	Organization = {Eurographics Association},
	Pages = {102--111},
	Title = {A multigrid solver for boundary value problems using programmable graphics hardware},
	Year = {2003}}

@article{buatois2007concurrent,
	Author = {Buatois, L. and Caumon, G. and L{\'e}vy, B.},
	Date-Added = {2010-08-19 15:45:02 -0500},
	Date-Modified = {2010-08-19 15:45:02 -0500},
	Journal = {High Performance Computing and Communications},
	Pages = {358--371},
	Publisher = {Citeseer},
	Title = {Concurrent number cruncher: {A}n efficient sparse linear solver on the {GPU}},
	Year = {2007}}

@article{joldes2010real,
	Author = {Joldes, G.R. and Wittek, A. and Miller, K.},
	Date-Added = {2010-08-19 15:44:41 -0500},
	Date-Modified = {2010-08-19 15:44:41 -0500},
	Journal = {Computer Methods in Applied Mechanics and Engineering},
	Publisher = {Elsevier},
	Title = {Real-time nonlinear finite element computations on {GPU}-application to neurosurgical simulation},
	Year = {2010}}

@misc{aharon2005gpu,
	Author = {Aharon, S.},
	Date-Added = {2010-08-19 15:44:32 -0500},
	Date-Modified = {2010-08-19 15:44:32 -0500},
	Month = apr # {~27},
	Note = {US Patent App. 11/115,642},
	Publisher = {Google Patents},
	Title = {{GPU}-based Finite Element},
	Year = {2005}}

@article{cevahir2009fast,
	Author = {Cevahir, A. and Nukada, A. and Matsuoka, S.},
	Date-Added = {2010-08-19 15:44:01 -0500},
	Date-Modified = {2010-08-19 15:44:01 -0500},
	Journal = {Computational Science--ICCS 2009},
	Pages = {893--903},
	Publisher = {Springer},
	Title = {Fast conjugate gradients with multiple {GPU}s},
	Year = {2009}}

@article{maier1995symmetric,
	Author = {Maier, G. and Miccoli, S. and Perego, U. and Novati, G.},
	Date-Added = {2010-08-19 15:43:57 -0500},
	Date-Modified = {2010-08-19 15:43:57 -0500},
	Journal = {Computational Mechanics},
	Number = {1},
	Pages = {115--129},
	Publisher = {Springer},
	Title = {Symmetric {G}alerkin boundary element method in plasticity and gradient plasticity},
	Volume = {17},
	Year = {1995}}

@article{corrigan-running,
	Author = {Corrigan, A. and Camelli, F. and L{\\"o}hner, R. and Wallin, J.},
	Date-Added = {2010-08-19 15:43:47 -0500},
	Date-Modified = {2010-08-19 15:43:47 -0500},
	Journal = {International Journal for Numerical Methods in Fluids},
	Publisher = {John Wiley \& Sons},
	Title = {Running unstructured grid based CFD solvers on modern graphics hardware}}

@inproceedings{Volkov08,
  author    = {Vasily Volkov and James W. Demmel},
  title     = {Benchmarking GPUs to tune dense linear algebra},
  booktitle = {Proceedings of the 2008 ACM/IEEE Conference on Supercomputing (SC08)},
  note      = {\url{http://mc.stanford.edu/cgi-bin/images/6/65/SC08_Volkov_GPU.pdf}},
  year      = {2008}
}

@techreport{cray-mvmult,
	author = "Guy~E. Blelloch and Michael~A. Heroux and Marco Zagha",
	title = "Segmented Operations for Sparse Matrix Computation
		 on Vector Multiprocessors",
	institution = "School of Computer Science, Carnegie Mellon University",
	number = "CMU-CS-93-173",
	month = aug,
	year = 1993}

@conference{bell2009implementing,
	Author = {Bell, N. and Garland, M.},
	Booktitle = {Proceedings of the Conference on High Performance Computing Networking, Storage and Analysis},
	Date-Added = {2010-08-19 15:43:42 -0500},
	Date-Modified = {2010-08-19 15:43:42 -0500},
	Organization = {ACM},
	Pages = {1--11},
	Title = {Implementing sparse matrix-vector multiplication on throughput-oriented processors},
	Year = {2009}}

@article{bell2008efficient,
	Author = {Bell, N. and Garland, M.},
	Date-Added = {2010-08-19 15:43:36 -0500},
	Date-Modified = {2010-08-19 15:43:36 -0500},
	Journal = {{NVIDIA} Corporation, {NVIDIA} Technical Report NVR-2008-004},
	Title = {Efficient sparse matrix-vector multiplication on {CUDA}},
	Year = {2008}}

@article{cohen-fast,
	Author = {Cohen, J. and Molemaker, M.J.},
	Date-Added = {2010-08-19 15:43:34 -0500},
	Date-Modified = {2010-08-19 15:43:34 -0500},
	Journal = {Parallel Computational Fluid Dynamics: Recent Advances and Future Directions},
	Pages = {414},
	Publisher = {DEStech Publications},
	Title = {A fast double precision CFD code using CUDA}}

@article{kazhdan2008streaming,
	Author = {Kazhdan, M. and Hoppe, H.},
	Date-Added = {2010-08-19 15:43:32 -0500},
	Date-Modified = {2010-08-19 15:43:32 -0500},
	Journal = {ACM Transactions on Graphics (TOG)},
	Number = {3},
	Pages = {21},
	Publisher = {ACM},
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	Year = {2008}}

@article{bonnet1998symmetric,
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@conference{zamith2007gpu,
	Author = {Zamith, M. and Clua, E. and Pagliosa, P. and Conci, A. and Montenegro, A. and Valente, L.},
	Booktitle = {Proceedings of the VI Brazilian Symposium on Computer Games and Digital Entertainment},
	Date-Added = {2010-08-19 15:43:14 -0500},
	Date-Modified = {2010-08-19 15:43:14 -0500},
	Pages = {37--43},
	Title = {The {GPU} used as a math co-processor in real time applications},
	Year = {2007}}

@article{baskaran2009optimizing,
	Author = {Baskaran, M.M. and Bordawekar, R.},
	Date-Added = {2010-08-19 15:42:56 -0500},
	Date-Modified = {2010-08-19 15:42:56 -0500},
	Journal = {IBM Research Report RC24704, IBM},
	Title = {Optimizing sparse matrix-vector multiplication on {GPU}s},
	Year = {2009}}

@misc{szeliski2006locally,
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	Date-Added = {2010-08-19 15:42:45 -0500},
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@article{jung2006cholesky,
	Author = {Jung, J.H. and O'Leary, D.P.},
	Date-Added = {2010-08-19 15:42:34 -0500},
	Date-Modified = {2010-08-19 15:42:34 -0500},
	Journal = {Scholarly Paper, University of Maryland},
	Publisher = {Citeseer},
	Title = {Cholesky decomposition and linear programming on a {GPU}},
	Year = {2006}}

@conference{filipovic2009gpu,
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	Booktitle = {SAAHPC: Symposium on Application Accelerators in HPC},
	Date-Added = {2010-08-19 15:42:33 -0500},
	Date-Modified = {2010-08-19 15:42:33 -0500},
	Title = {{GPU} Acceleration of Equations Assembly in Finite Elements Method-Preliminary Results},
	Year = {2009}}

@article{taylor2009modelling,
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	Date-Modified = {2010-08-19 15:42:23 -0500},
	Journal = {Medical Image Analysis},
	Number = {2},
	Pages = {234--244},
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	Title = {On modelling of anisotropic viscoelasticity for soft tissue simulation: Numerical solution and {GPU} execution},
	Volume = {13},
	Year = {2009}}

@conference{owens2007survey,
	Author = {Owens, J.D. and Luebke, D. and Govindaraju, N. and Harris, M. and Kr{\\"u}ger, J. and Lefohn, A.E. and Purcell, T.J.},
	Booktitle = {Computer Graphics Forum},
	Date-Added = {2010-08-19 15:42:21 -0500},
	Date-Modified = {2010-08-19 15:42:21 -0500},
	Number = {1},
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	Pages = {80--113},
	Title = {A survey of general-purpose computation on graphics hardware},
	Volume = {26},
	Year = {2007}}

@article{strzodka2005scientific,
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	Journal = {Simulation Modelling Practice and Theory},
	Number = {8},
	Pages = {667--680},
	Publisher = {Elsevier},
	Title = {Scientific computation for simulations on programmable graphics hardware},
	Volume = {13},
	Year = {2005}}

@conference{rumpf2001using,
	Author = {Rumpf, M. and Strzodka, R.},
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	Date-Added = {2010-08-19 15:42:15 -0500},
	Date-Modified = {2010-08-19 15:42:15 -0500},
	Organization = {Citeseer},
	Pages = {193--202},
	Title = {Using graphics cards for quantized FEM computations},
	Year = {2001}}

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	Number = {2},
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	Volume = {35},
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@article{tejada2005large,
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	Journal = {Simulation Modelling Practice and Theory},
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	Pages = {703--715},
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	Title = {Large steps in {GPU}-based deformable bodies simulation},
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	Year = {2005}}

@article{goddeke2008using,
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	Date-Added = {2010-08-19 15:42:06 -0500},
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	Year = {2008}}

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	Date-Added = {2010-08-19 15:41:51 -0500},
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@article{abedi2006space,
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@conference{georgii2005interactiveb,
	Author = {Georgii, J. and Westermann, R.},
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	Year = {2005}}

@article{mosegaard2005gpu,
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	Date-Added = {2010-08-19 15:41:35 -0500},
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	Publisher = {IEEE Computer Society},
	Title = {{GPU} accelerated surgical simulators for complex morphology},
	Year = {2005}}

@article{meyer2007particle,
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	Pages = {1015--1026},
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@conference{rumpf2001nonlinear,
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	Date-Added = {2010-08-19 15:41:29 -0500},
	Date-Modified = {2010-08-19 15:41:29 -0500},
	Organization = {Springer Verlag Wien},
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	Title = {Nonlinear diffusion in graphics hardware},
	Year = {2001}}

@article{georgii2005interactive,
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	Organization = {Springer-Verlag},
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	Title = {Real-time nonlinear finite element analysis for surgical simulation using graphics processing units},
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@conference{kakadiaris1994active,
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@conference{de2004gpu,
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	Year = {2004}}

@book{taflove1995computational,
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@conference{galoppo2005lu,
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@conference{ryoo2008optimization,
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	Date-Added = {2010-08-19 15:41:12 -0500},
	Date-Modified = {2010-08-19 15:41:12 -0500},
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	Year = {2008}}

@conference{micikevicius20093d,
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	Date-Modified = {2010-08-19 15:41:11 -0500},
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	Year = {2009}}

@conference{zhou2004pixel,
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	Year = {2009}}

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@article{wu2005improved,
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	Date-Added = {2010-08-19 15:40:59 -0500},
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	Year = {2005}}

@article{taylor2008high,
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@conference{bolz2003sparse,
	Author = {Bolz, J. and Farmer, I. and Grinspun, E. and Schr{\\"o}oder, P.},
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	Date-Added = {2010-08-19 15:40:55 -0500},
	Date-Modified = {2010-08-19 15:40:55 -0500},
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@article{wu2004hybrid,
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	Journal = {Computer Animation and Virtual Worlds},
	Number = {3-4},
	Pages = {219--227},
	Publisher = {John Wiley \& Sons},
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	Year = {2004}}
% ----------------------------------------------------------------------------------------------------------------

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@ARTICLE{WO-2000,
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        TITLE = "Verification and Validation of the 3D Finite Element Transport Theory
                 Code {EVENT} for Shielding Applications",
        JOURNAL = "J. Nucl. Sci. and Tech.",
        VOLUME = "Supplement 1",
        PAGES = "466--470",
        YEAR = "2000"
}

@unpublished{GNEP-WEB,
        AUTHOR = "{U.S. Department of Energy}",
        TITLE = "Global Nuclear Energy Partnership ({GNEP})",
        NOTE = "\url{ http://www.gnep.energy.gov}",
        YEAR = "2007"
}

@Book{LEWIS-MILLER-1984,
  AUTHOR    = "E. E. Lewis and W. F. Miller, Jr.",
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  ADDRESS   = "",
  PUBLISHER = "Wiley",
  YEAR	    = "1984"
}

@Article{couple1,
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  year      = 1959,
  pages = "113--115",
  volume = "2(1)"
}

@inproceedings{weber1,
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        TITLE = "Coupled {CFD/CSM} vibration design methodology for generation {IV} long-life fuel and component design",
        BOOKTITLE = "4th International Conference on Supercomputing in Nuclear Applications",
        YEAR = "2000"
}

@Misc{gnep:report,
  author =       "Phillip Finck and David Keyes and Rick Stevens",
  title =        "{Report on the {DOE} Joint {NE/SC} Workshop Simulation and Modeling for Advanced Nuclear Energy Systems}",
  year = 2006
}

@Misc{subsurface-workshop-ref,
  author =       "D. {Zachman (Chair)}",
  title =        "{Computational Subsurface Sciences Workshop}",
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}

@Misc{fusion:report,
  title =  "{Report of the Fusion Energy Sciences Advisory Committee Burning Plasma Strategy Panel}",
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  year = 2002,
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}

@Misc{hecrtf:report,
  title = "{Report of the High End Computing Revitalization Task Force (HECRTF)}",
  key = "HECRTF",
  year = 2004,
  howpublished = "see \url{http://www.ostp.gov/nstc/html/HECRTF-FINAL_051004.pdf}"
}

@Misc{doesc20years,
  title = "{Facilities for the Future of Science: A Twenty-Year Outlook}",
  key = "Office of Science, U.S. Department of Energy",
  year = 2003,
  howpublished = "Office of Science, U.S. Department of Energy,
     see \url{http://www.sc.doe.gov/Scientific_User_Facilities/History/20-Year-Outlook-screen.pdf}"
}

@phdthesis{karpeev-thesis,
  author = "D. A. Karpeyev",
  title =  "Geometric Integrators for Hamiltonian PDEs",
  school = "Old Dominion University",
  year = "2002",
}


@incollection{fjp:ima,
  AUTHOR=    "Lori Freitag and Mark Jones and Paul Plassmann",
  title = "The Scalability of Mesh Improvement Algorithms",
  booktitle = "Algorithms for Parallel Processing",
  publisher = "Springer-Verlag",
  volume = "105",
  series = "The IMA Volumes in Mathematics and Its Applications",
  editor = "Michael T.\ Heath and Abhiram Ranade and Robert S.\ Schreiber",
  year = "1998",
  pages = "185--212"
  }

@inproceedings{poet,
        AUTHOR = "Rob Armstrong and Alex Cheung",
        TITLE = "{POET} ({P}arallel {O}bject-Oriented {E}nvironment and {T}oolkit)
       and Frameworks for Scientific Distributed Computing",
        BOOKTITLE = "Proceedings of {HICSS97}",
        YEAR = "1997",
}

@Misc{ pseware-web-page,
  author =       "",
  title =        "{PSEware} {Web} page",
  note =         "\url{http://www.extreme.indiana.edu/pseware}, Indiana University",
  key =        "{PSEware} {Web} page",
}

@article{epperly2011high,
  title={High-performance language interoperability for scientific computing through {B}abel},
  author={Epperly, Thomas GW and Kumfert, Gary and Dahlgren, Tamara and Ebner, Dietmar and Leek, Jim and Prantl, Adrian and Kohn, Scott},
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  pages={1094342011414036},
  year={2011},
  publisher={SAGE Publications}
}

@Misc{ babel-web-page,
  author =       "Tom Epperly and Tamara Dahlgren and Gary Kumfert",
  title =        "{Babel} {Web} page",
  note =         "\url{http://www.llnl.gov/CASC/components/babel.html}",
}

@Misc{ infospheres-web-page,
  author =       "K.~M. {Chandy et al.}",
  title =        "{Infospheres} {W}eb page",
  note =         "\url{http://www.infospheres.caltech.edu}",
  key =        "{Infospheres} {Web} page",
}

@misc{ hammond,
  author =       "Glenn Hammond",
  title =        "{Sandia National Laboratory}, {C}omputations on {R}eactive {F}low, private communication"
}

@misc{ ornl,
  author = "Oak Ridge National Laboratory",
  title =        "Private communication via petsc-maint email support"
}

@Unpublished{ cumulvs-web-page,
  author =       "",
  title =        "{Cumulvs} {W}eb page",
  note =         "http://www.epm.ornl.gov/cs/cumulvs.html",
  key =        "{Cumulvs} {W}eb page",
}

@Article{nonlinearGMRES,
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  title     = "Krylov Subspace Acceleration for Nonlinear Multigrid Schemes",
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  year      = 1997,
  pages = "271--290",
  volume = "6"
}

@Article{pcice,
  author    = "Richard C. Martineau and Ray A. Berry",
  title     = "The pressure-corrected ICE finite element method for compressible flows on unstructured meshes",
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  year      = 2004,
  pages = "659--685",
  volume = "198(2)"
}

@Article{cumulvs97,
  author    = "G. A. Geist and J. A. Kohl and P. M. Papadopoulos",
  title     = "{CUMULVS}: Providing Fault-Tolerance, Visualization,
                  and Steering of Parallel Applications",
  journal =   "International Journal of Supercomputing Applications",
  year      = 1997
}
@techreport{daly2012interagency,
  author={John Daly and Bill Harrod and Thuc Hoang and Lucy Nowell and Bob Adolf and Shekhar Borkar and Nathan DeBardeleben and Mootaz Elnozahy and Mike Heroux and David Rogers and Rob Ross and Vivek Sarkar and Martin Schulz and Marc Snir and Paul Woodward},
  title={Inter-Agency Workshop on HPC Resilience at Extreme Scale},
  year=2012,
  publisher={US Department of Defense}
}

@Article{karpeev1,
  author    = "A. L. Islas and D. A. Karpeev and C. M. Schober",
  title     = {Geometric Integrators for the Nonlinear Schr\"odinger Equation},
  journal =   "J. Comp. Phys.",
  year      = 2001,
  pages     = "116--148",
  volume    = 173
}

@InProceedings{scirun97,
  author    = "S. G. Parker and D. W. Weinstein and C. R. Johnson",
  title     = "The {SCIRun} Computational Steering System",
  booktitle = "Modern Software Tools in Scientific Computing",
  editor    = "E. Arge and A. M. Bruaset and H. P. Langtangen",
  publisher = "Birkhauser Press",
  year      = 1997,
}

@techreport{ szyld,
 AUTHOR=    "Valeria Simoncini and Daniel B. Szyld",
 TITLE=     " Theory of Inexact Krylov Subspace Methods and Applications to Scientific Computing",
 year      = "2002",
 institution =  "Department of Mathematics, Temple University",
 number =     "02-4-12"
}

@techreport{ pdelab,
 AUTHOR=    "S. Weerawarana and E. N. Houstis and J. R. Rice and A. C. Catlin and
             C. Crabill and C. C. Chui and S. Markus",
 TITLE=     "{PDELab}: An Object-Oriented Framework for Building Problem Solving
            Environments for {PDE} Based Applications",
 year      = 1994,
 institution =  "Department of Computer Sciences, Purdue University",
 number =     "CSD-TR-94-021"
}

@Unpublished{ilu-web-page,
  author = "Bill Janssen and Mike Spreitzer and Dan Larner and Chris Jacobi",
  title = 	 "{I}nter-{L}anguage {U}nification Reference Manual",
  note = 	 "ftp://ftp.parc.xerox.com/ilu/ilu.html, Xerox Corporation",
}

@Unpublished{doe2k-web-page,
  title = 	 "{DOE2000 Initiative} {W}eb page",
  note = 	 "http://www.mcs.anl.gov/DOE2000",
  key = 	 "DOE2000 Initiative",
}

@Misc{pvode-web-page,
  title = 	 "{PVODE} {W}eb Page",
  note = 	 "\url{http://www.llnl.gov/CASC/PVODE},
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  author =	 "A. {Hindmarsh et al.}",
}

@BOOK{szyperski97,
       AUTHOR = "Clemens Szyperski",
       TITLE = "Component Software: Beyond Object-Oriented Programming",
       PUBLISHER = "ACM Press",
       address = "New York",
       YEAR = 1997
}

@Unpublished{isis++-web-page,
  title = 	 "{ISIS++} {W}eb Page",
  note = 	 "http://ca.sandia.gov/isis",
  author =	 "Robert L. Clay and Kyran Mish and Alan B. Williams",
  Institution = "Sandia National Laboratories",
}

@Unpublished{petsc:coloringuse,
  title = 	 "Code for computing sparse {J}acobians",
  note = 	 "\url{http://www.mcs.anl.gov/petsc/miscellaneous/external.html}",
  Institution = "Argonne National Laboratory"
}

@Unpublished{petsc:external,
  author =       {B. F. {Smith et al.}},
  title =        "{External Software Used by PETSc}",
  note =         "\url{http://www.mcs.anl.gov/petsc/miscellaneous/external.html}",
  Institution = "Argonne National Laboratory"
}

@Unpublished{petsc:use-by-external-packages,
  author =       {B. F. {Smith et al.}},
  title =        "{Software Packages that Use or Interface to PETSc}",
  note =         "\url{http://www.mcs.anl.gov/petsc/publications/petscapps.html#packages}",
  Institution = "Argonne National Laboratory"
}

@Unpublished{petsc:prizes,
  author =       {B. F. {Smith et al.}},
  title =        "{Prizes Won Using PETSc}",
  note =         "\url{http://www.mcs.anl.gov/petsc/publications/prizes.html}",
  Institution = "Argonne National Laboratory"
}

@Unpublished{petsc:csgf,
  author =       {B. F. {Smith et al.}},
  title =        "{DOE Computational Science Graduate Fellowship (CSGF) Users of PETSc}",
  note =         "\url{http://www.mcs.anl.gov/petsc/publications/prizes.html}",
  Institution = "Argonne National Laboratory"
}

@Unpublished{flash-web-page,
  title = 	 "{U}niversity of {C}hicago {C}enter on {A}strophysical
                  {T}hermonuclear {F}lashes {W}eb Page",
  note = 	 "http://www.asci.uchicago.edu",
  author =       "R. {Rosner et al.}",
  Institution = "University of Chicago",
}

@Unpublished{esi-web-page,
  title = 	 "{E}quation {S}olver {I}nterface {F}orum {W}eb Page",
  note = 	 "http://z.ca.sandia.gov/esi",
  author =       "R. {Clay et al.}",
}

@Unpublished{infobus-web-page,
  title = 	 "{I}nfo{B}us {W}eb Page",
  note = 	 "http://www.java.sun.com/beans/infobus",
  key =          "infobus"
}

@Unpublished{xray-web-page,
  title = 	 "{S}upercomputer {S}olution of {M}assive
                  {C}rystallographic and {M}icrotomographic {S}tructural {P}roblems {W}eb Page ({DOE} Grand Challenge Project)",
  note = 	 "http://www.mcs.anl.gov/xray/",
  Institution = "Argonne National Laboratory",
}



@INPROCEEDINGS{ kohn98,
 AUTHOR=    "Andrew Cleary and Scott Kohn and Steven Smith and Brent Smolinski",
 TITLE=     "Language Interoperability Mechanisms for High-Performance Scientific Applications",
 PUBLISHER= "SIAM",
 BOOKTITLE= "Proceedings of the SIAM Workshop on Object Oriented Methods for
                Inter-operable Scientific and Engineering Computing",
 year      = 1999,
 pages     = "30-39"
}

@INPROCEEDINGS{ kohn01,
 AUTHOR=    "Scott Kohn and Gary Kumfert and Jeff Painter and Cal Ribbens",
 TITLE=     "Divorcing Language Dependencies from a Scientific Software Library",
 PUBLISHER= "SIAM",
 BOOKTITLE= "Proceedings of the Tenth SIAM Conference on Parallel Processing",
 year      = 2001,
}


@INPROCEEDINGS{ freitag_jones_plassmann98,
 AUTHOR=    "Lori Freitag and Mark Jones and Paul Plassmann",
 TITLE=     "Component Integration for Unstructured Mesh Algorithms and Software",
 PUBLISHER= "SIAM",
 BOOKTITLE= "Proceedings of the SIAM Workshop on Object Oriented Methods for
                Inter-operable Scientific and Engineering Computing",
 year      = 1999,
 pages     = "215-224",
}

@BOOK{templates,
       AUTHOR = {R. Barrett and M. Berry and T. F. Chan and J. Demmel and J. Donato and J. Dongarra and V. Eijkhout
       and R. Pozo and C. Romine and H. Van der Vorst },
       TITLE = {Templates for the Solution of Linear Systems: Building Blocks for Iterative Methods},
       PUBLISHER = {SIAM},
       YEAR = {1994},
       ADDRESS = {Philadelphia, PA}
 }

@InProceedings{parasha2,
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     booktitle = {SC97 Proceedings},
    publisher = "IEEE Computer Society Press",
     year = {1997}
}

@TECHREPORT{parasha,
        AUTHOR="M. Parashar and J. C. Browne",
        TITLE="{DAGH}: A Data-Management Infrastructure for Parallel
                  Adaptive Mesh Refinement Techniques",
        INSTITUTION="Department of Computer Science, University of
                  Texas at Austin",
        YEAR="1995"
                }

@Article{parti,
  author =       {R. Das and M. Uysal and J. Saltz and Y. S. Hwang},
  title =        {Communication Optimizations for Irregular
                  Scientific Computations on Distributed Memory Architectures},
  journal =      {Journal of Parallel and Distributed Computing},
  year =         {1994},
  volume =       {22},
  pages =        {462--478}
}

@Article{mparti,
  author =       {G. Agrawal and A. Sussman and J. Saltz},
  title =        {An Integrated Runtime and Compile-time Approach for
                  Parallelizing Structured and Block Structured Applications},
  journal =      {IEEE Trans. on Parallel and Distributed Systems},
  volume =       {6},
  number =       {7},
  year =         "1995"
}

@Article{gropp-lusk-doss-skjellum,
  author =       { William Gropp and Ewing Lusk and Nathan Doss and Anthony
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  title =        {A high-performance, portable implementation of the {MPI}
                  Message Passing Interface standard},
  journal =      {Parallel Computing},
  year =         1996,
  volume =       22,
  pages =        {789--828}
}

@InProceedings{lam,
  author    = "Greg Burns and Raja Daoud and James Vaigl",
  title     = "{LAM}: An Open Cluster Environment for {MPI}",
  booktitle = "Proceedings of Supercomputing Symposium '94",
  editor    = "John W. Ross",
  publisher = "University of Toronto",
  pages     = "379--386",
  year      = 1994,
}


@Article{cs99,
  author    = "X.-C. Cai and M. Sarkis",
  title     = "A restricted additive {S}chwarz preconditioner for general sparse linear systems",
  journal =   "SIAM J. Scientific Computing",
  year      = "1999",
  volume    = "21",
  pages     = "792-797"
}

@TechReport( cs97a,
    AUTHOR  = "X.-C. Cai and M. Sarkis",
    TITLE   = "A restricted additive {S}chwarz preconditioner for general sparse linear systems ",
    YEAR    = 1997,
    Institution  = "Computer Science Department,
University of Colorado-Boulder",
    Number = "CU-CS 843-97",
    Note= "(accepted by SIAM J. of Scientific  Computing)"
    )

@article{cai2003restricted,
  title={Restricted additive {S}chwarz preconditioners with harmonic overlap for symmetric positive definite linear systems},
  author={Cai, X.C. and Dryja, M. and Sarkis, M.},
  journal={SIAM Journal on Numerical Analysis},
  volume=41,
  issue=1,
  pages={1209--1231},
  year=2003,
  doi={10.1137/S0036142901389621}
}

@TECHREPORT{caisaad,
        AUTHOR="Xiao-Chuan Cai and Youcef Saad",
        TITLE="Overlapping domain decomposition algorithms for
               general sparse matrices",
        INSTITUTION="Army High Performance Computing
                     Research Center, University of Minnesota ",
        YEAR="1993",
        NUMBER="Preprint 93-027 ",
        NOTE= "SIAM J. Sci. Comp. (submitted)"
                }

@BOOK{ruminations,
      AUTHOR="Andrew Koenig and Barbara Moo",
      TITLE="Ruminations on C++",
      YEAR="1996",
      PUBLISHER="Addison-Wesley"
      }

@BOOK{mpi-complete,
      AUTHOR="Marc Snir and Steve Otto and Steven Huss-Lederman and David
                  Walker and Jack Dongarra",
      TITLE="{MPI}: The Complete Reference",
      YEAR="1995",
      PUBLISHER="MIT Press"
      }


@Unpublished{ tcl-tk-web-page,
  title = 	 "{Tcl/Tk} {W}orld {W}ide {W}eb page",
  note = 	 "http://www.sunlabs.com/research/tcl/",
  year =	 1996,
  month =	 Aug
}

@misc{mpich-web-page,
  author = {William Gropp and {et. al.}},
  title  = {{MPICH} {W}eb page},
  key    = "MPICH",
  url    = {http://www.mpich.org},
  howpublished = {\url{http://www.mpich.org}},
}

@Article{ MPI-final,
	Title = "{MPI}: A Message-Passing Interface Standard",
        Journal = "International J. Supercomputing Applications",
        Volume  = 8,
	Number = "3/4",
	Year = 1994,
	Key = "MPI Standard - final"
}

@Unpublished{ npb-web-page,
  key =          "NAS Parallel Benchmarks",
  title = 	 "{NAS} {P}arallel {B}enchmarks {W}eb page",
  note = 	 "http://www.nas.nasa.\-gov/\-NAS/\-NPB/\-index.html",
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  month =	 Dec
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@book{ george81,
	TITLE = "Computer Solution of Large Sparse Positive Definite Systems",
	AUTHOR= "Alan George and Joseph W. Liu",
	PUBLISHER = "Prentice-Hall",
	YEAR      = 1981,
	KEY       = "SparseDirect"
        }

@book{ p4-book,
	TITLE     = "Portable Programs for Parallel Processors",
	PUBLISHER = "Holt, Rinehart, {and} Winston",
	YEAR      = 1987,
	AUTHOR    = "James Boyle and Ralph Butler and Terrence Disz and
	             Barnett Glickfeld and Ewing Lusk and Ross Overbeek and
		     James Patterson and Rick Stevens",
	KEY       = "P4Book"
        }

@Article{stones,
  author = 	"H. L. Stone",
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  volumne = 5,
  Year =        1968
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@Article{parallelstones,
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  volumne = 13,
  Year =        2001
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@Article{p4-paper,
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  Year =        1993
}

@TechReport(picl,
    Author=      "G.~A.~Geist and Michael~T.~Heath and B.~W.~Peyton and
	          Patrick~H.~Worley",
    Title=       "{PICL}: A portable instrumented communications library",
    Institution= "Oak Ridge National Laboratory",
    Number=      "TM-11130",
    Year=        "1990",
    Key=         "PICL")


@TechReport( upshot,
    Author=      "Virginia Herrarte and Ewing Lusk",
    Title=       "Studying Parallel Program Behavior with {U}pshot",
    Institution= "Argonne National Laboratory",
    Number=      "ANL-91/15",
    Month=       AUG,
    Year=        "1991",
    Key=         "Upshot" )

@TechReport( p4-manual,
    Author=      "Ralph Butler and Ewing Lusk",
    Title=       "User's Guide to the p4 Parallel Programming System",
    Institution= "Argonne National Laboratory",
    Number=      "ANL-92/17",
    Month=       Oct,
    Year=        "1992",
    Key=         "p4-Manual" )

@inproceedings{oldparti,
    Author    =      "Gagan Agrawal and Alan Sussman and Joel Saltz",
    Title     =       "Compiler and Runtime Support for Unstructured and Block
                  Structured Problems",
    BOOKTITLE = "Proceedings of Supercomputing '93",
    pages     = "578--587",
    YEAR      = "1993"
}

@article{parti2,
    Author    =      "S. S. Mukherjee and S. D. Sharma and
                      M. DF. Hill and J. R. Larus and A. Rogers and J. Saltz",
    Title     =       "Efficient Support for Irregular Applications on
                  Distributed Memory Machines",
    journal   = "ACM SIGPLAN Notices",
    YEAR      = "1995",
    pages     = "68-79",
    volume    = "30",
    number    = "8"
}


@article{parti3,
    Author    =      "J. Saltz and R. Mirchandaney and K. Crowley",
    Title     =       "Run-Time Parallelization and Scheduling of Loops",
    journal   = "IEEE Trans. Computers",
    YEAR      = "1991",
    pages     = "604-612",
    volume    = "40",
    number    = "5"
}

@inproceedings{disz-lusk:wamtrace,
	AUTHOR = "Terrence Disz and Ewing Lusk",
	TITLE = "A Graphical Tool for Observing the Behavior of Parallel
 		Logic Programs",
	BOOKTITLE = "Proceedings of the 1987 Symposium on Logic Programming",
	YEAR = "1987",
	PAGES = "46--53"
}
@inproceedings{gorlick-kesselman:gauge,
	AUTHOR = "Michael Gorlick and Carl Kesselman",
	TITLE = "Timing {Prolog} programs without Clocks",
	BOOKTITLE = "Proceedings of the 1987 Symposium on Logic Programming",
	YEAR = "1996",
        publisher = "Birkhauser"
}


@TechReport( aztec,
    Author = "Scott A. Hutchinson and John N. Shadid and Ray S. Tuminaro",
    Title  = "Aztec User's Guide Version 1.1",
    Institution = "Sandia National Laboratories",
    Month  = Oct,
    Year   = 1995,
    Number = "SAND95/1559"
    )

@TechReport( aztec2,
    Author = "Ray S. Tuminaro and Micheal Heroux and Scott A. Hutchinson and John N. Shadid",
    Title  = "Official {Aztec} User's Guide Version 2.1",
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    Year   = 1999,
    )

@Book{taylor-chandy:pcn,
    Author = "Chandy, M. and Taylor, S.",
    Title = "An Introduction to Parallel Programming",
    Year = 1991,
    Publisher = "Jones and Bartlett"}

@Book{foster-taylor:strand,
    Title = "Strand:  New Concepts in Parallel Programming",
    Author = "Ian Foster and Stephen Taylor",
    Publisher = "Prentice-Hall",
    Adress = " Englewood Cliffs, New Jersey",
    Year = 1990}

@article{aurora,
	AUTHOR = "E. Lusk and R. Butler and T. Disz and R. Olson and
		R. Overbeek and R. Stevens and D.H.D. Warren and
		A. Calderwood and P. Szeredi and S. Haridi and
		P. Brand and M. Carlsson and A. Ciepielewski and
		B. Hausman",
	TITLE = "The Aurora OR-Parallel Prolog System",
	JOURNAL = "New Generation Computing",
	VOLUME = 7,
	NUMBER = 3,
	YEAR = 1990,
	PAGES = "243--271"
}

@Techreport{roo,
    Author = "E. Lusk and W. McCune and J. Slaney",
    Title = "Roo---a Parallel Theorem Prover",
    Institution = "Argonne National Laboratory",
    Number = "MCS--TM--149",
    Year = 1991}

@Techreport{heath-etheridge:vppp,
    Author = "M. T. Heath and J. A. Etheridge",
    Title = "Visualizing the Performance of Parallel Programs",
    Institution = "Oak Ridge National Laboratory",
    Number = "ORNL TM-11813",
    Year = 1991}


@Techreport{chem:vis,
  Author = "Ewing L. Lusk",
  Title = "Performance Visualization for Parallel Programs",
  Institution = "Argonne National Laboratory",
  Number = "ANL/MCS--P287--0192",
  Year = 1991,
  Note = "(to appear in {\em Theoretica Chimica Acta})"
  }

@Techreport{picltrace,
    Author = "P.~H.~Worley",
    Title = "A new {PICL} trace file format",
    Institution = "Oak Ridge National Laboratory",
    Number = "ORNL TM-12125",
    Month  = JUN,
    Year = 1992}

@inproceedings{hideo,
	AUTHOR = "Gary Olsen and Carl Woese and Ray Hagstrom and Hideo Matsuda
		  and Ross Overbeek",
	TITLE = "Inference of Phylogenetic trees using maximum likelihood",
	BOOKTITLE = "Proceedings of the First Intel Delta Applications
		     Workshop",
	YEAR = "1992",
	PAGES = "247--262"
}

@InProceedings(DW90,
    Author=      "M. Dryja and O. Widlund",
    Title=       "Towards a Unified Theory of Domain Decomposition Algorithms
                  for Elliptic Problems",
    Booktitle=   "Third International Symposium on Domain Decomposition
                  Methods",
    Editor=      "T. F. Chan and R. Glowinski
                 and J. P\'eriaux and O. B. Widlund",
    Year=        "1990",
    Pages=       "3-21",
    Publisher=   "SIAM",
    Address=     "Philadelphia",
    Annote=      "Additive {S}chwarz.  Surveys recent (1989) results; some
		  comments on 3-d and how many approaches may be cast in
		  the form of additive {S}chwarz-subspace form.  58
	          references, good introduction to the theory.  No
	          computations",
    Key=         "DryjaWidlund90 !AS")

@UnPublished(rosing,
    Author=    "Matt Rosing and Joel Saltz",
    Title=     "Low Latency Messages on Distributed Memory Multiprocessors",
    Key=       "LowLatency",
    Note=      "manuscript, 1992")

@techreport{jp:incomplete,
         AUTHOR = "Mark T. Jones and Paul E. Plassmann",
        TITLE = "An Improved Incomplete {C}holesky Factorization",
        INSTITUTION = "Argonne National Laboratory",
        ADDRESS = "Argonne, IL",
        TYPE = "Preprint",
        NOTE = "(to appear in {\em ACM Trans. on Mathematical Software, 1995})",
        NUMBER = "MCS-P206-0191",
        YEAR = "1991",
	KEY = "jones" }

@incollection{jp:ima,
  AUTHOR = "Mark Jones and Paul Plassmann",
  title = "The Efficient Parallel Iterative Solution
  of Large Sparse Linear Systems",
  booktitle = "Graph Theory and Sparse Matrix Computation",
  publisher = "Springer-Verlag",
  series = "The IMA Volumes in Mathematics and Its Applications",
  editor = "Alan George and John Gilbert and Joseph W.H.~Liu",
  volume = "56",
  year = "1993",
  pages="229--245"
  }

@Article{ pw98,
  AUTHOR = "M. Pernice and H. F. Walker",
  TITLE = "{NITSOL}: A {Newton} Iterative Solver for Nonlinear Systems",
  journal =	 "SIAM J. Sci. Stat. Comput.",
  year =	 1998,
  volume =	 19,
  pages =	 "302--318"
}

@TechReport( ysmp83,
    KEY       =   "Eisenstat",
    AUTHOR    =   "S.~C.~Eisenstat and H.~C.~Elman and M.~H.~Schultz and
		  A.~H.~Sherman",
    TITLE     =   "The (New) {Y}ale {S}parse {M}atrix {P}ackage",
    INSTITUTION=  "Department of Computer Science, Yale University",
    NUMBER    =   "YALE/DCS/RR-265",
    MONTH     =    APR,
    YEAR      =   "1983"
    )

@inbook( ysmp84,
    AUTHOR    =   "S.~C.~Eisenstat and H.~C.~Elman and M.~H.~Schultz and
		  A.~H.~Sherman",
    chapterTITLE     =   "The (New) {Y}ale {S}parse {M}atrix {P}ackage",
    title = "Elliptic Problem Solvers II",
    publisher = "Academic Press",
    pages = "45--52",
    editors = "G. Birkhoff and A. Schoenstadt",
    YEAR      =   "1984"
    )

@TechReport{ sparsekit,
    KEY       = "Saad",
    AUTHOR    = "Youcef Saad",
    TITLE     = "{SPARSKIT}, a basic tool kit for sparse matrix computations",
    INSTITUTION= "Center for Supercomputing Research and Development,
	          University of Illinois at Urbana-Chanpaign",
    NUMBER    = "1029",
    YEAR      = 1990
    }

@TechReport( pde-user-ref,
    Author = "Barry F. Smith",
    Title  = "Extensible {PDE} Solvers Package Users Manual",
    Institution = "Argonne National Laboratory",
    Month  = SEP,
    Year   = 1994,
    Number = "ANL-93/40",
    Key    = "Smith94 ! PDE"
    )

@TechReport( bs-user-ref,
    Author = "Mark T. Jones and Paul E. Plassmann",
    Title  = "{BlockSolve95} Users Manual: Scalable Library Software for
                  the Parallel Solution of Sparse Linear Systems",
    Institution = "Argonne National Laboratory",
    Month  = DEC,
    Year   = 1995,
    Number = "ANL-95/48"
    )

@TechReport( snes-user-ref,
    Author = "William D. Gropp and Lois Curfman McInnes and Barry F. Smith",
    Title  = "Using the {S}calable {N}onlinear {E}quations {S}olvers Package",
    Institution = "Argonne National Laboratory",
    Month  = Feb,
    Year   = 1995,
    Number = "ANL/MCS-TM-193",
    Key    = "GroppMcInnesSmith95 ! SNES"
    )

@TechReport( sles-user-ref,
    Author = "William D. Gropp and Barry F. Smith",
    Title  = "{S}implified {L}inear {E}quation {S}olvers Users Manual",
    Institution = "Argonne National Laboratory",
    Month  = MAR,
    Year   = 1993,
    Number = "ANL-93/8",
    Key    = "GroppSmith93 ! SLES"
    )
@TechReport( chameleon-user-ref,
    Author = "William D. Gropp and Barry F. Smith",
    Title  = "Chameleon Parallel programming tools Users Manual",
    Institution = "Argonne National Laboratory",
    Month  = MAR,
    Year   = 1993,
    Number = "ANL-93/23",
    Key    = "GroppSmith93 ! Chameleon"
    )

@Article( euclid2,
    Author = "D. Hysom and A. Pothen",
    Title  = "A Scalable Parallel Algorithm For Incomplete Factor Preconditioning",
    Journal = "SIAM J. Sci. Comput.",
    Volume  = 22,
    Number  = 6,
    Pages   = "2194--2215"
)

@TechReport( euclid1,
    Author = "D. Hysom and A. Pothen",
    Title  = "Euclid User Manual (A Scalable {ILU} Preconditioning Library for the Parallel Solution of Sparse Linear Systems)",
    Institution = "Old Dominion University",
    Year   = "2001"
    )

@TechReport( ksp-user-ref,
    Author = "William D. Gropp and Barry F. Smith",
    Title  = "Users Manual for {KSP}: Data-Structure-Neutral Codes Implementing {K}rylov Space Methods",
    Institution = "Argonne National Laboratory",
    Month  = AUG,
    Year   = 1993,
    Number = "ANL-93/30",
    Key    = "GroppSmith93 ! KSP"
    )


@TechReport( mpi-chameleon,
    Author = "William D. Gropp and Ewing Lusk",
    Title  = "A Test Implementation of the {MPI} Draft Message-Passing
	     Standard",
    Institution = "Argonne National Laboratory",
    Month  = DEC,
    Year   = 1992,
    Number = "ANL-92/47",
    Key    = "GroppLusk92 ! MPI"
    )

@TechReport( blockcomm-fortran,
    Author = "William D. Gropp",
    Title  = "Block{C}omm for {F}ortran",
    Institution = "Argonne National Laboratory",
    Month  = MAY,
    Year   = 1993,
    Number = "ANL-93/00 (to appear)",
    Key    = "Gropp93 ! BlockComm"
    )

@TechReport( autodocument,
    Author = "William D. Gropp",
    Title  = "Automatic documentation of {C} programs",
    Institution = "Argonne National Laboratory",
    Month  = MAY,
    Year   = 1993,
    Number = "ANL-93/00",
    Key    = "Gropp93 ! Autodoc"
    )

@TechReport( zipcode,
    Author = "Anthony Skjellum and Steven G. Smith and Charles H Still and
Alvin P. Leung and Manfred Morari",
    Title  = "The {Z}ipcode message-passing system",
    Institution = "Lawrence Livermore National Laboratory",
    Month  = SEP,
    Year   = 1992,
    Number = "Unpublished",
    Key    = "Skjellum92 ! Zipcode" )

@Article( paragraph,
    Author = "Michael T. Heath and Jennifer Etheridge Finger",
    Title  = "Visualizing performance of parallel programs",
    Journal = "IEEE Software",
    Volume  = 8,
    Number  = 5,
    Month   = SEP,
    Year    = 1991,
    Pages   = "29--39",
    Key     = "Heath91 ! Paragraph" )

@article( gropp90,
    Author = "William Gropp and Edward Smith",
    Title  = "Computational Fluid Dynamics on Parallel Processors",
    Journal = "Computers and Fluids",
    Volume  = 18,
    Year    = 1990,
    Pages   = "289--304",
    Key     = "Gropp90 ! performance" )

@article( foster92,
    Author = "Ian Foster and William Gropp and Rick Stevens",
    Title  = "The parallel scalability of the spectral transform method",
    Journal = "Monthly Weather Review",
    Volume  = 120,
    Year    = 1992,
    Pages   = "835--850",
    Key     = "Foster92 ! performance" )

@INBOOK{fgn,
        AUTHOR="R. Freund and G. H. Golub and N. Nachtigal",
        TITLE="Iterative Solution of Linear Systems",
        SERIES="Acta Numerica",
        YEAR="1992",
        PUBLISHER="Cambridge University Press",
        PAGES="57--100"
                }

@TechReport( nachtigal90,
    Author = "No{\"e}l M. Nachtigal and Satish C. Reddy and Lloyd N. Trefethen",
    Title  = "How Fast are Nonsymmetric Matrix Iterations?",
    Institution = "Massachusetts Institute of Technology",
    Month  = MAR,
    Year   = 1990,
    Number = "90-2",
    Key    = "Nachtigal | Krylov"
    )
@article{nachtigal1992fnm,
  title={How Fast are Nonsymmetric Matrix Iterations?},
  author={Nachtigal, N.M. and Reddy, S.C. and Trefethen, L.N.},
  journal={SIAM Journal on Matrix Analysis and Applications},
  volume={13},
  pages={778},
  year={1992},
  publisher={SIAM}
}
@techreport{embree1999descriptive,
  title={How descriptive are {GMRES} convergence bounds},
  author={Embree, M.},
  year={1999},
  number={08},
  institution={Oxford University Computing Laboratory}
}

@Article{ vorst92,
  author = 	 "H. van der Vorst",
  title = 	 "Bi-{CGSTAB}: A fast and smoothly converging varient of
		  {Bi-CG} for the solution of nonsymmetric linear systems",
  journal =	 "SIAM J. Sci. Stat. Comput.",
  year =	 1992,
  volume =	 13,
  pages =	 "631--644"
}

@Article{ eisenstat81,
  author = 	 "S. Eisenstat",
  title = 	 "Efficient Implementation of a Class of {CG} Methods",
  journal =	 "SIAM J. Sci. Stat. Comput.",
  year =	 1981,
  volume =	 2,
  pages =	 "1--4"
}

@Manual{ ibm-essl,
    Title = "{E}ngineering and {S}cientific {S}ubroutine {L}ibrary Version 2:
Guide and Reference",
    Organization = "IBM",
    Year  = 1992,
    Key   = "IBM-ESSL"
    }

@Manual{ IBM-EUI,
    Title = "{IBM} {AIX} Parallel Environment Parallel Programming Subroutine
Reference Release 2.0",
    Organization = "IBM",
    Month = JUN,
    Year  = 1994,
    Key   = "IBM-EUI"
    }

@Manual( IBM-EUIH,
    Title = "Using {EUIH}: An Experimental {EUI} Implementation",
    Organization = "IBM",
    Author = "Peter Hochschild",
    Year  = 1993,
    Key   = "IBM-EUIH"
    )

@TechReport{ MPI,
	Title = "Document for a Standard Message-Passing Interface",
	Author = "Message Passing Interface Forum",
	Institution =  "University of Tennessee",
	Number = "CS-93-214",
	Month  = NOV,
	Year = 1993,
	Key = "MPI Standard"
}

@Unpublished{ mpi-final-web,
  author = 	 "Message Passing Interface Forum",
  title = 	 "{MPI}: A Message-Passing Interface Standard",
  note = 	 "http://www.mcs.anl.gov/mpi/mpi-report/mpi-report.html",
  year =	 1994,
  month =	 MAY
}


@Book{hockney-jesshope,
  author = 	 "R. W. Hockney and C. R. Jesshope",
  title = 	 "Parallel Computers 2",
  publisher = 	 "Adam Hilger",
  year = 	 "1988"
}

@Book{cm-fortran,
  author = 	 "{Thinking Machines Corporation}",
  title = 	 "Users Manual for CM-Fortran",
  publisher = 	 "Thinking Machines Corporation",
  year = 	 1993
}

@TechReport{ Chang93,
	Title = "Experiments and Bounds on Block Diagonal Preconditioning",
	Author = "Mark Yan-Ming Chang and Martin H. Schultz",
	Institution = "Yale Department of Computer Science",
	Number = "YALEU/DCS/RR-994",
	Month  = NOV,
	Year   = 1993,
	Key    = "BDD|diag" }

@inproceedings{gropplevine93,
	AUTHOR = "N. Galbreath and W. Gropp and D. Levine",
	TITLE = "Applications-Driven Parallel {I/O}",
	BOOKTITLE = "Proceedings of Supercomputing '93",
	YEAR = "1993",
	PAGES = "462--471"
}

@book{ Siegle85,
AUTHOR = "H. J. Siegel",
TITLE  = "Interconnection Networks for Large Scale Parallel Processing",
PUBLISHER = "Lexington Books",
YEAR      = 1985,
KEY       = "Network Comparison"
}

@article{ Lawrie75,
AUTHOR = "D. H. Lawrie",
TITLE  = "Access and alignment of data in an array processor",
JOURNAL = "IEEE Transactions on Computers",
VOLUME  = "C-24",
NUMBER  = 12,
MONTH   = DEC,
YEAR    = 1975,
PAGES   = "1145--1155",
KEY     = "Omega Network"
}

@book{Knuth1986,
  title  = {The {\TeX}{Book}},
  author = {Donald Ervin Knuth and Duane Bibby},
  volume = {1993},
  year   = {1986},
  publisher = {Addison-Wesley Reading, Massachusetts}
}

@book{ Lamport86,
AUTHOR = "Leslie Lamport",
TITLE  = "{LaTeX}: A document preparation system",
PUBLISHER = "Addison-Wesley",
YEAR      = 1986,
KEY       = "Latex Manual"
}

@TechReport( tohtml,
    Author=      "William Gropp",
    Title=       "Users Manual for tohtml: Producing true hypertext
documents from {LaTeX}",
    Institution= "Argonne National Laboratory",
    Number=      "ANL/MCS-TM-00",
    Month=       JAN,
    Year=        "1995",
    Key=         "tohtml" )

@TechReport( doctext,
    Author=      "William Gropp",
    Title=       "Users Manual for doctext:
Producing documentation from {C} source code",
    Institution= "Argonne National Laboratory",
    Number=      "ANL/MCS-TM-00",
    Month=       JAN,
    Year=        "1995",
    Key=         "doctext" )

@TechReport( bfort,
    Author=      "William Gropp",
    Title=       "Users Manual for bfort:
Producing {F}ortran interfaces to {C} source code",
    Institution= "Argonne National Laboratory",
    Number=      "ANL/MCS-TM-208",
    Month=       MAR,
    Year=        "1995",
    Key=         "doctext" )


@InProceedings{ gropp-lusk:unix-tools,
    Author=     "William Gropp and Ewing Lusk",
    Title=      "Scalable {U}nix Tools on Parallel Processors",
    Booktitle=  "Proceedings of the 1994 Scalable High Performanc Computing
		  Conference",
    Publisher=  "IEEE",
    Pages    =  "56--62"
    }

@inproceedings{jp:bell_prize,
  AUTHOR = "Mark Jones and Paul Plassmann",
    TITLE = "Solution of Large, Sparse Systems of Linear Equations
    in Massively Parallel Applications",
    booktitle = "Proceedings of Supercomputing '92",
    publisher = "IEEE Computer Society Press",
    YEAR = "1992",
    Pages = "551--560"
    }


@comment{WEB, CWEB references (for doctext)}
@TechReport{ web,
  author = 	 "Donald E. Knuth",
  title = 	 "The {\tt WEB} system of structured documentation",
  institution =  "Computer Science Department, Stanford University",
  year = 	 1983,
  number =	 980,
  month =	 SEP
}

@Article{ literatepgm,
  author = 	 "Donald E. Knuth",
  title = 	 "Literate Programming",
  journal =	 "Computer Journal",
  year =	 1984,
  volume =	 27,
  number =	 2,
  pages =	 "91--111"
}

@Unpublished{ cweb-code,
  author = 	 "Silvio Levy and Donald E. Knuth",
  title = 	 "CWEB",
  note = 	 "CWEB is available at ftp://pip.shsu.edu/tex-archive/web/c\_cpp/cweb"
}

@Article( componentware:94,
    AUTHOR  = "Jon Udell",
    TITLE   = "Componentware",
    JOURNAL = "Byte",
    VOLUME  = "May",
    PAGES   = "46-56",
    YEAR    = 1994,
    KEY     = "Udell94 ! componentware"
    )

@article{jp:scalable,
  AUTHOR = "Mark Jones and Paul Plassmann",
  TITLE = "Scalable Iterative Solution of Sparse Linear Systems",
  Journal = "Parallel Computing",
  Volume = "20",
  Number = "5",
  Month = "May",
  YEAR = "1994",
  Pages = "753--773"
  }

@article{jp:pcolor,
  AUTHOR = "Mark T. Jones and Paul E. Plassmann",
  Title = "A Parallel Graph Coloring Heuristic",
  journal = "SIAM J. Sci. Comput.",
  Volume = "14",
  Number = "3",
  Pages = "654-669",
  Year = "1993",
  }

@TechReport( block_solve,
    AUTHOR      = "Mark T. Jones and Paul E. Plassmann",
    TITLE       = "{B}lock{S}olve v1.1:  Scalable Library Software for
                   the Parallel Solution of Sparse Linear Systems",
    INSTITUTION = "Argonne National Laboratory",
    YEAR        = 1992,
    NUMBER      = "ANL-92/46",
    KEY     = "JonesPlassmann92 ! block_solve"
    )

@book{ optguide93,
   TITLE	= "Optimization Software Guide",
   AUTHOR	= "Jorge J. Mor\'{e} and Stephen J. Wright",
   PUBLISHER	= "SIAM Publications",
   ADDRESS	= "Philadelphia",
   YEAR		= 1993,
   }

@inproceedings{ more84,
   AUTHOR	= "Jorge J. Mor\'{e} and Danny C. Sorenson and
		   Burton S. Garbow and Kenneth E. Hillstrom",
   TITLE	= "The {MINPACK} Project",
   BOOKTITLE	= "Sources and Development of Mathematical Software",
   EDITOR	= "Wayne R. Cowell",
   YEAR		= 1984,
   PAGES	= "88-111"
   }

@inproceedings{ supercond,
   AUTHOR	= "Lois Curfman Mc{I}nnes and Mario Palumbo",
   TITLE	= "Parallel Solution of the Anisotropic
		   {G}inzburg-{L}andau Model",
   BOOKTITLE	= "Proceedings of the Toward Teraflop Computing and New
		   Grand Challenge Applications Conference",
   MONTH	= Feb,
   YEAR		= "1994",
   KEY     	= "McInnesPalumbo94 ! superconductivity "
   }

@Article( steihaug:83,
    AUTHOR  = "Trond Steihaug",
    TITLE   = "The Conjugate Gradient Method and Trust Regions in
               Large Scale Optimization",
    JOURNAL = "SIAM J. Numer. Anal.",
    VOLUME  = 20,
    YEAR    = 1983,
    PAGES   = "626-637",
    KEY     = "steihaug92 ! trust_region"
    )

@Unpublished( preosti:93,
    AUTHOR  = "Gianfranco Preosti",
    TITLE   = " ",
    NOTE    = "Unpublished information, {P}hysics {D}epartment,
               {P}urdue {U}niversity",
    YEAR    = 1993,
    KEY     = "preosti93 ! GL-tilt3d"
    )

@Unpublished( more:93,
    AUTHOR  = "Jorge J. Mor\'{e}",
    TITLE   = " ",
    NOTE    = "Unpublished information, {M}athematics and
               {C}omputer {S}cience {D}ivision,
               {A}rgonne {N}ational {L}aboratory",
    YEAR    = 1993,
    KEY     = "more93 ! MINPACK-2"
    )

@TechReport( minpack2test,
    AUTHOR      = "Brett M. Averick and Richard G. Carter and
                   Jorge J. Mor\'{e}",
    TITLE       = "The {MINPACK-2} Test Problem Collection",
    INSTITUTION = "Argonne National Laboratory",
    YEAR        = 1991,
    NUMBER      = "ANL/MCS-TM-150",
    KEY     = "more91 ! MINPACK-2"
    )

@TechReport{ hohmann:94,
    AUTHOR      = "Andreas Hohmann",
    TITLE       = "Object Oriented Design of Multilevel {N}ewton and
		   Continuation Methods",
    INSTITUTION = "Konrad-Zuse-Zentrum fur Informationstechnik Berlin",
    YEAR        = 1994,
    NUMBER      = "SC-94-4",
    KEY         = "Hohmann94"
    }

@TechReport{ meza:94,
    AUTHOR      = "Juan C. Meza",
    TITLE       = "{OPT}++:  An Object-Oriented Class Library for
		  Nonlinear Optimization",
    INSTITUTION = "Sandia National Laboratory",
    YEAR        = 1994,
    NUMBER      = "SAND94-8225",
    KEY         = "Meza94"
    }

@book{dennis:83,
   AUTHOR       = "Dennis, Jr., J. E. and Robert B. Schnabel",
   TITLE        = "Numerical Methods for Unconstrained Optimization and
                   Nonlinear Equations",
   PUBLISHER    = "Prentice-Hall",
   ADDRESS      = "Englewood Cliffs, NJ",
   YEAR         = {1983}
   }

@TechReport{more:92,
    AUTHOR      = "Jorge J. Mor\'{e} and David Thuente",
    TITLE       = "Line search algorithms with guaranteed sufficient decrease",
    INSTITUTION = "Mathematics and Computer Science Division, Argonne National Laboratory",
    YEAR        = 1992,
    NUMBER      = "MCS-P330-1092",
    }

@Article{brownsaad:90,
  author = 	 "Peter N. Brown and Youcef Saad",
  title = 	 "Hybrid {K}rylov Methods for Nonlinear Systems of Equations",
  journal =	 "SIAM J. Sci. Stat. Comput.",
  year =	 1990,
  volume =	 11,
  pages =	 "450-481"
}

@Book{using-mpi,
  author = 	 "William Gropp and Ewing Lusk and Anthony Skjellum",
  title = 	 "Using MPI: Portable Parallel Programming with the Message
		  Passing Interface",
  publisher = 	 "MIT Press",
  year = 	 1994
}

@Book{using-mpi2,
  author = 	 "William Gropp and Ewing Lusk  and Rajeev Thakur",
  title = 	 "Using MPI 2: Advanced Features of the Message Passing Interface",
  publisher = 	 "MIT Press",
  year = 	 1999
}


@article{hs:52,
   author="Magnus R. Hestenes and Eduard Steifel",
   title="Methods of Conjugate Gradients for Solving Linear Systems",
   journal="J. Research of the National Bureau of Standards",
   year=1952,
   volume=49,
   pages="409-436"}

@article{ss:86,
   author="Youcef Saad and Martin H. Schultz",
   title="{GMRES}:  A Generalized Minimal Residual Algorithm
           for Solving Nonsymmetric Linear Systems",
   journal = "SIAM J. Sci. Stat. Comput.",
   year=1986,
   volume=7,
   pages="856-869"}

@article{so:89,
   author="Peter Sonneveld",
   title="{CGS}, A Fast {L}anczos-type Solver for Nonsymmetric Linear
          Systems",
   journal = "SIAM J. Sci. Stat. Comput.",
   year=1989,
   volume=10,
   pages="36-52"}

@article{v:92,
   author="{H. A.} {van der Vorst}",
   title="{B}i{CGSTAB}:  A fast and smoothly converging variant
          of {B}i{CG} for the solution of nonsymmetric linear
                  systems",
   journal = "SIAM J. Sci. Stat. Comput.",
   volume=13,
   year=1992,
   pages="631-644"}

@article{f:93,
   author="Roland W. Freund",
   title="A Transpose-Free Quasi-Minimal Residual Algorithm for
          Non-{H}ermitian Linear Systems",
   journal = "SIAM J. Sci. Stat. Comput.",
   volume=14,
   year=1993,
   pages="470-482"}

@article{ish:89,
  author="S. Ishizuka",
  title="An Experimental Study on Extinction and
         Stablity of Tubular Flames",
  journal="Combustion and Flame",
  volume=75,
  year=1989,
  pages="367-379"}

@book{williams89,
  TITLE = "Combustion Theory, The
           Fundamental Theory of Chemically Reacting Flow Systems",
  AUTHOR= "F.A. Williams",
  PUBLISHER = "Addison-Wesley",
  YEAR      = 1989,
  pages     = "367-379"}

@book{RA75,
author = {R. Aris},
title = {The Mathematical Theory of Diffusion and
Reaction in Permeable Catalysts},
publisher = {Oxford},
year = {1975}
}

@book{Bebernes89,
author = {J. Bebernes and D. Eberly},
title = {Mathematical Problems from Combustion Theory},
publisher = {Springer-Verlag},
series = {Applied Mathematical Sciences 83},
year = {1989}
}

@inproceedings{Kikuchi89,
author = {F. Kikuchi},
booktitle = { Computing Methods in Applied Sciences and Engineering},
editor = {R. Glowinski and J. L. Lions},
publisher = {Springer-Verlag},
series = {Lecture Notes in Mathematics},
title = {Finite element approximations to bifurcation
problems of turning point type},
year = {1977}
}

@article{RG85,
   author="R. Glowinski and H.B. Keller and L. Reinhart",
   title="Continuation-conjugate Gradient Methods fo the Least Squares
                  Solution of Nonlinear Boundary Problems",
   journal = "SIAM J. Sci. Stat. Comput.",
   volume=6,
   year=1985,
   pages="793-832"}

@InProceedings{whitfield91,
  author    = "D. Whitfield and L. Taylor",
  title     = "Discretized {N}ewton-Relaxation Solution of High
                  Resolution Flux-Difference Split Schemes",
  booktitle = "Proceedings of the AIAA Tenth Computational Fluid Dynamics Conference",
  misc      = "AIAA-91-1539",
  pages     = "134-145",
  year      = 1991,
}


@INPROCEEDINGS{Quinlan1,
 AUTHOR=    "M. Lemke and D. Quinlan",
 TITLE=     "P++, a {C}++ Virtual Shared Grids Based Programming
             Environment for Architecture-Independent Development of
                  Structured Grid Applications",
 BOOKTITLE= "CONPAR/VAPP V, Lecture Notes in Computer Science",
 PUBLISHER= "Springer Verlag",
 YEAR=      "1992"
}


@INPROCEEDINGS{Quinlan2,
 AUTHOR=    "R. Parsons and D. Quinlan",
 TITLE=     "A++/{P}++ Array Classes for Architecture Independent Finite
            Difference Computations",
 BOOKTITLE= "Proceedings of the Second Annual Object-Oriented Numerics
             Conference",
 YEAR=      "1994"
}

% *****  Overview of functionality in Diffpack

@inbook{DPoverview,
 author = "Bruaset, A. M. and Langtangen, H. P.",
 booktitle = "Mathematical Models and Software Tools in Industrial
           Mathematics",
 title = "A Comprehensive Set of Tools for Solving Partial Differential
           Equations; {Diffpack}",
 publisher = "Birkh{\"{a}}user",
 pages = "61--90",
 year = 1997}


% *****  Short overview of Diffpack

@incollection{DPoverview2,
 author = "Bruaset, A. M. and Langtangen, H. P.",
 editor = "A. Sydow",
 booktitle = "Proceedings of the 15th IMACS World Congress
              on Scientific Computation, Modelling and Applied Mathematics",
 title = "Diffpack: A Software Environment for Rapid Prototyping of
          {PDE} Solvers",
 pages = "553--558",
 volume = 4,
 year = 1997}


% *****  Comprehensive documentation of Diffpack and
%        associated numerical methods:




@Book{DPbook,
  author =  "H. P. Langtangen",
  title =   "Numerical Solution of Partial Differential Equations;
             Models, Algorithms and Software. Part I",
  series =  "Lecture Notes in Computational Science and Engineering",
  publisher =    "Springer-Verlag",
  year =         "1998"
}

% *****  Design issues of the linear solvers in Diffpack, serves also as a
%        collection of examples on O-O in numerical computing

@article{AmbHpl97a,
     author =   "A. M. Bruaset and H. P. Langtangen ",
     title  =   "Object-Oriented Design of Preconditioned Iterative
                  Methods in {Diffpack}",
     journal = "Transactions on Mathematical Software",
     volume = {23 },
     pages = "50--80",
     year = {1997}
}

@misc{DPURL,
      author  = "{Diffpack Web page}",
      howpublished = "\url{http://www.diffpack.com}"
}


% *****  General intro to object-oriented numerics for "FORTRAN programmers"

@incollection{OONintro,
 author = "Arge, E. and Bruaset, A. M. and H. P. Langtangen",
 editor = "D{\ae}hlen, M. and Tveito, A.",
 booktitle = "Mathematical Models and Software Tools in Industrial Mathematics",
 title = "Object-Oriented Numerics",
 publisher = "Birkh{\"{a}}user",
 year = 1997}


% *****  Efficiency comparison: BLAS 1, Diffpack, C,
%        and finite element applications (F77 vs Diffpack)

@incollection{DPefficiency,
 author = "Arge, E. and Bruaset, A. M. and Calvin, P. B. and
          Kanney, J. F. and Langtangen, H. P. and Miller, C. T.",
 editor = "D{\ae}hlen, M. and Tveito, A.",
 booktitle = "Mathematical Models and Software Tools in Industrial
             Mathematics",
 title = "On the Efficiency of {C++} in Scientific Computing",
 publisher = "Birkh{\"{a}}user",
 pages = "91--118",
 year = 1997}

% ***** Parallel concept in Diffpack:

@incollection{DPparallel,
 author = "A.~M.~Bruaset and X. Cai and H. P. Langtangen and A. Tveito",
 editor = "Y. Ishikawa and R. R. Oldehoeft and J. V. W. Reynders and M. Tholburn",
 booktitle = "Scientific Computing in Object-Oriented Parallel Environments",
 title = "Numerical Solution of {PDE}s on Parallel Computers Utilizing
          Sequential Simulators",
 publisher = "Springer--Verlag",
 series = "Lecture Notes in Computer Science",
 pages = "161--168",
 year = 1997}

% ***** DD and ML methods in Diffpack:

@incollection{DPDDML,
 author = "A.~M.~Bruaset and H. P. Langtangen and G. W. Zumbusch",
 editor = "P. Bj{\o}rstad and M. Espedal and D. Keyes",
 booktitle = "Proceedings of the 9th Conference on Domain
              Decomposition",
 title = "Domain decomposition and multilevel methods in Diffpack",
 year = 1997}

@inproceedings{bsca98,
 author=    "David L. Bruhwiler and Svetlana G. Shasharina and John R. Cary and David Alexander",
 title=     "Design and Implementation of an Object Oriented C++ Library for Nonlinear Optimization",
 booktitle= "Proceedings of the SIAM Workshop on Object Oriented Methods for
             Inter-operable Scientific and Engineering Computing",
 editor=   "Mike Henderson et al.",
 pages=     "165-173",
 year=      "1998"
}



@BOOK{scalapack-user-guide,
       AUTHOR = "L. S. Blackford and J. Choi and A. Cleary and E. D'Azevedo and
                 J. Demmel and I. Dhillon and J. Dongarra and S. Hammarling and
                 G. Henry and A. Petitet and K. Stanley and D. Walker and R. C. Whaley",
       TITLE = "Sca{LAPACK} Users' Guide",
       PUBLISHER = "SIAM",
       ADDRESS = "Philadelphia, PA",
       YEAR = 1997
}

@INPROCEEDINGS{KEYES99,
        AUTHOR = "D. E. Keyes",
        TITLE = "How Scalable is Domain Decomposition in Practice?",
        BOOKTITLE = "Proceedings of the 11th International Conference on
                     Domain Decomposition Methods",
        EDITOR = "C.-H. Lai et al.",
        PUBLISHER = "Domain Decomposition Press, Bergen",
        NOTE = "To appear",
        YEAR = "1999" }

@article{fun3d,
author="W. K. Anderson and D. L. Bonhaus",
title="An implicit upwind algorithm for computing turbulent flows on unstructured grids",
journal="Computers and Fluids",
year=1994,
volume=23,
pages="1--21"
}

% -------------------------------------------------------------------------
% -------------------------------------------------------------------------

@Article(torczon,
    Author=      "Dennis, Jr., J. E. and V.~Torczon",
    Title=       "Direct Search Methods on Parallel Machines",
    Journal=     "SIAM J. Optimization",
    Volume=      1,
    Pages=       "448--474",
    Year=        1991,
    Key=         "Torczon !PDS")

@InProceedings{WT91,
  author    = "D. L. Whitfield and L. K. Taylor",
  title     = "Discretized {N}ewton-Relaxation Solution of High
                  Resolution Flux-Difference Split Schemes",
  booktitle = "Proceedings of the AIAA Tenth Annual Computational Fluid Dynamics Conference",
  misc      = "AIAA-91-1539",
  pages     = "134-145",
  year      = 1991,
}

@article{EW96,
author="S. C. Eisenstat and  H. F. Walker",
title="Choosing the forcing terms in an inexact {N}ewton method",
journal="SIAM J. Scientific Computing",
volume=17,
year=1996,
pages="16--32"
}

@Book{thi93,
  author = 	 "{Thinking Machines Corporation}",
  title = 	 "Users Manual for CM-Fortran",
  publisher = 	 "Thinking Machines Corporation",
  year = 	 1993
}

@Book{mortonmayers94,
  author = 	 "K. W. Morton and D. F. Mayers",
  title = 	 "Numerical Solution of Partial Differential Equations",
  publisher = 	 "Press Syndicate of the University of Cambridge",
  year = 	 1994
}

@Book{heath97,
  author = 	 "Michael T. Heath",
  title = 	 "Scientific Computing: An Introductory Survey",
  publisher = 	 "McGraw Hill",
  year = 	 1997
}

@Article{captools96,
  author    = "C. S. Ierotheou and S. P Johnson and M. Cross and P. F. Leggett",
  title     = "Computer Aided Parallelization Tools ({CAPTools}) - Conceptual
               Overview and Performance on the Parallelization of Structured Mesh Codes",
  journal   = "Parallel Computing",
  volume    = 22,
  pages     = "197-226",
  year      = 1996
}


@Unpublished{ nastran-web-page,
  Author = "{MSC Software Corporation}",
  title = 	 "{NASTRAN} {W}eb page",
  note = 	 "See {\tt http://www.mechsolutions.com\-/products\-/nastran/}"
}

@Book{hpf,
  author = 	 "C. H. Koelbel and D. B. Loveman and R. S. Schreiber and G. L. Steele and M. E. Zosel",
  title = 	 "The High Performance Fotran Handbook",
  publisher = 	 "MIT Press",
  year = 	 "1994"
}

@inproceedings{keyes98,
        AUTHOR     = "D. E. Keyes",
        TITLE      = "Trends in Algorithms for Nonuniform Applications on Hierarchical Distributed Architectures",
        BOOKTITLE  = "Proceedings of the Workshop on Computational Aerosciences for the 21st Century",
        EDITORS    = "M. D. Salas and  W. K. Anderson",
        PPUBLISHER = "Elsevier",
        YEAR       = "1998"
}

@inproceedings{cca99,
        AUTHOR = "R. Armstrong and D. Gannon and A. Geist and K. Keahey and
                  S. Kohn and L. C. McInnes and S. Parker and B. Smolinski",
        TITLE = "Toward a Common Component Architecture for High-Performance
                 Scientific Computing",
        BOOKTITLE = "Proceedings of {High Performance Distributed Computing}",
        pages = "115--124",
        YEAR = "1999",
}


@inproceedings{pooma-atlas,
author = "S. Atlas and S. Banerjee and J. C. Cummings and P. J. Hinker and
M. Srikant and J. V. W. Reynders and M. Tholburn",
title = "{POOMA}: A High-Performance Distributed Simulation Environment for
Scientific Applications",
year = 1995,
month = "December",
Booktitle = "Supercomputing '95 Proceedings",
}

% ---------------------------------------------------------------------------------
% New bib entries for CRPC paper

@misc {
   mgnet-web-page,
   author = "Craig C. Douglas",
   title  = "{MGNet Web page}",
   note   = "See {\tt http://\-www.mgnet.org}"
}

@misc {
   dagh-web-page,
   author = "M. Parashar and J. C. Browne",
   title  = "{DAGH Web page}",
   note   = "\url{http://www.caip.rutgers.edu/~parashar/DAGH}"
}

@misc {
   parasol-web-page,
   key    = "PARASOL",
   title  = "{PARASOL Web page}",
   note   = "See {\tt http://\-www.genias.de/\-projects/\-parasol}"
}

@misc {
   pooma-web-page,
   author  = "{POOMA Web page}",
   note   = "See {\tt http://\-www.acl.lanl.gov/pooma}"
}

@misc {
   mudpack-web-page,
   author = "John C. Adams",
   title  = "{MUDPACK Web page}",
   note   = "See {\tt http://\-www.scd.ucar.edu/\-css/\-software/\-mudpack}"
}

@misc {
   pellpack-web-page,
   author = "Elias Houstis and John Rice and Apostolos Hadjidimos",
   title  = "{Parallel ELLPACK Web page}",
   note   = "See {\tt http://\-www.cs.purdue.edu/\-research/\-cse/\-pellpack/}"
}

@inproceedings{pellpack95,
        AUTHOR = "E. N. Houstis and S. B. Kim and S. Markus and P. Wu and
                  N. E. Houstis and A.C. Catlin and S. Weerawarana and T.S. Papatheodorou",
        TITLE = "Parallel {ELLPACK} Elliptic {PDE} Solvers",
        BOOKTITLE = "Proceedings of INTEL Supercomputer User's Group Conference",
        ADDRESS = "Albuquerque, NM",
        YEAR = "1995",
}

@misc {
   nhse-web-page,
   author  = "{National High-Performance Software Exchange Web page}",
   note   = "See {\tt http://\-www.nhse.org}"
}

@misc {
   doug-web-page,
   author = "Mark J. Hagger and Linda Stals",
   title  = "{DOUG Web Page}",
   note   = "See {\tt http://\-www.maths.bath.ac.uk/\~{ }parsoft/\-doug/}"
}

@TECHREPORT{doug97,
        AUTHOR="Mark J. Hagger",
        TITLE="Automatic Domain Decomposition on Unstructured Grids {(DOUG)}",
        INSTITUTION="Mathematical Sciences, University of Bath",
        YEAR="1997",
        NUMBER="9706",
        NOTE= "Advances in Computational Mathematics (to appear)"
        }

@misc {
   ug-web-page,
   author  = "{UG Web Page}",
   note   = "See {\tt http://\-cox.iwr.uni-heidelberg.de/\~{ }ug/}"
}

@Article{ug97,
  author    = "P. Bastian and K. Birken and K. Johannsen and S. Lang and N. Neuss and
               H. Rentz-Reichert and C. Wieners",
  title     = "{UG} -- A Flexible Software Toolbox for Solving Partial Differential Equations",
  journal =   "Computing and Visualization in Science",
  year      = "1997",
  volume    = "",
  pages     = ""
}

@misc {
   vecfem-web-page,
   author = "Lutz Grosz",
   title  = "{VECFEM Web Page}",
   note   = "See {\tt http://\-wwwmaths.anu.edu.au/\-\~{ }vecfem/}"
}

@misc{atlas-web-page,
   author = {R. Clint {Whaley et al.}},
   title  = {{ATLAS Web Page}},
   howpublished = {\url{http://math-atlas.sourceforge.net}}
}

@misc {fenics-web-page,
   author = "Todd Dupont and Johan Hoffman and Johan Jansson and Claes Johnson and Robert C. Kirby and Matthew Knepley and Mats Larson and Anders Logg and Ridgway Scott",
   title  = "{FEniCS Web Page}",
   note   = "\url{http://www.fenicsproject.org}",
   year   = "2005"
}

@misc{matlab-web-page,
  author = {{The} {MathWorks}},
  title  = {{Matlab} {Web} page},
  url    = {http://www.mathworks.com}
}

@misc {
   phipac-web-page,
   author = "J. A. Bilmes and K. Asanovic and R. Vudoc and S. Iyer and
             J. Demmel and C. Chin and D. Lam",
   title  = "{PHiPAC Web Page}",
   note   = "See {\tt http://\-www.icsi.berkeley.edu/\-\~{ }bilmes/\-phipac/}"
}

@inproceedings{kelp,
    Author    = "Stephan J. Fink and Scott B. Baden and Scott R. Kohn",
    title     = "Flexible Communication Mechanisms for Dynamic Structured Applications",
    BOOKTITLE = "Irregular '96",
    YEAR      = "1996"
}

@Unpublished{ kelp-web-page,
  author =       "Scott Baden",
  title = 	 "{KeLP} {W}eb page",
  note = 	 "See {\tt http://\-www-cse.ucsd.edu/\-groups/\-hpcl/\-scg/\-kelp/}",
}

@inproceedings {
   hk99,
   author    = "R. Hornung and S. Kohn",
   title     = "The Use of Object-Oriented Design Patterns in the {SAMRAI}
                Structured {AMR} Framework",
   booktitle = "Proceedings of the SIAM Workshop on Object-Oriented Methods
                for Inter-Operable Scientific and Engineering Computing",
   pages     = "235-244",
   year      = 1999,
   note      = "See \url{http://www.llnl.gov/CASC/samrai}"
}

@Unpublished{samrai-web-page,
  title   = "{SAMRAI} {W}eb Page",
  author = "Scott Kohn and Xabier Garaiza and Rich Hornung and Steve Smith",
  note      = "See {\tt http://www.llnl.gov/\-CASC/SAMRAI}",
}


@Misc{overture-web-page,
  author = "William Henshaw and Kyle Chand",
  title  = "{Overture} {W}eb page",
  howpublished = "\url{http://www.llnl.gov/CASC/Overture}"
}

@INPROCEEDINGS{ overture99,
 AUTHOR=    "D.L. Brown and W.D. Henshaw and D.J. Quinlan",
 TITLE=     "Overture: An Object-Oriented Framework for Solving Partial Differential Equations
             on Overlapping Grids",
 PUBLISHER= "SIAM",
 BOOKTITLE= "Proceedings of the SIAM Workshop on Object Oriented Methods for
                Inter-operable Scientific and Engineering Computing",
 year      = 1999,
 pages     = "215-224",
 note      = "See \url{http://www.llnl.gov/CASC/Overture}"
}

@inProceedings{diffpack,
    Author = "A.M. Bruaset and H.P. Langtangen",
    Title = "A Comprehensive Set of Tools for Solving Partial
                  Differential Equations: {D}iffpack",
    BOOKTITLE = "Numerical Methods and Software Tools in Industrial Mathematics",
    Year = 1997,
    pages = "61--90",
    Publisher = "Birkhauser Press"}

@Article{Dongarra:1984:ILA,
   author =       "J. J. Dongarra and F. G. Gustavson and A. Karp",
   title =        "Implementing Linear Algebra Algorithms for Dense
                  Matrices on a Vector Pipeline Machine",
   journal =      "SIAM Review",
   volume =       "26",
   number =       "1",
   pages =        "91--112",
   month =        jan,
   year =         "1984",
   coden =        "SIREAD",
   ISSN =         "0036-1445 (print), 1095-7200 (electronic)",
   mrclass =      "65F10 (65F30)",
   mrnumber =     "85c:65032",
   bibdate =      "Mon Jan 20 1997",
   abstract =     "The authors examine common implementations of linear
                  algebra algorithms, such as matrix-vector
                  multiplication, matrix-matrix multiplication and the
                  solution of linear equations. The different versions
                  are examined for efficiency on a computer architecture
                  which uses vector processing and has pipelined
                  instruction execution. By using the advanced
                  architectural features of such machines, one can
                  usually achieve maximum performance, and tremendous
                  improvements in terms of execution speed can be seen
                  over conventional computers.",
   classification = "723; 921",
   journalabr =   "SIAM Rev",
   keywords =     "computer programming --- Algorithms; dense matrices;
                  linear algebra algorithms; mathematical programming;
                  vector pipeline machine",
}

@BOOK{qv99,
       AUTHOR = "Alfio Quarteroni and Alberto Valli",
       TITLE = "Domain Decomposition Methods for Partial Differential Equations",
       PUBLISHER = "Oxford Science Publications",
       address = "Oxford",
       YEAR = 1999
}

@BOOK{ksv97,
       EDITOR = "David E. Keyes and Ahmed Sameh and V. Venkatakrishnan",
       TITLE = "Parallel Numerical Algorithms",
       PUBLISHER = "Kluwer Academic Publishers",
       address = "the Netherlands",
       YEAR = 1997
}

@BOOK{hackbusch94,
       AUTHOR = "Wolfgang Hackbusch",
       TITLE = "Iterative Solution of Large Sparse Systems of Equations",
       PUBLISHER = "Springer-Verlag",
       address = "New York",
       YEAR = 1994
}

@article{hackbusch1980fast,
  title={Fast solution of elliptic control problems},
  author={Hackbusch, W.},
  journal={Journal of Optimization Theory and Applications},
  volume={31},
  number={4},
  pages={565--581},
  year={1980},
  publisher={Springer}
}

@book{hackbusch1985multi,
  title={{Multi-grid methods and applications}},
  author={Hackbusch, W.},
  isbn={3540127615},
  issn={0179-3632},
  year={1985},
  publisher={Springer Verlag}
}

@BOOK{axelsson94,
       AUTHOR = "Owe Axelsson",
       TITLE = "Iterative Solution Methods",
       PUBLISHER = "Cambridge University Press",
       address = "Cambridge",
       YEAR = 1994
}

@BOOK{saad96,
       AUTHOR = "Yousef Saad",
       TITLE = "Iterative Methods for Sparse Linear Systems",
       PUBLISHER = "PWS Publishing Company",
       address = "Boston",
       YEAR = 1996
}
@book(saad2003,
       author="Yousef Saad",
      title={Iterative Methods for Sparse Linear Systems, 2nd edition},
      Publisher="SIAM", address="Philadelpha, PA",
     year="2003"
)

@book{vandervorst03,
   author = "Henk A. {van der Vorst}",
   title = "Iterative Krylov Methods for Large Linear Systems",
   publisher = "Cambridge Monographs on Applied ahd Computational Mathematics",
   year = 2003
}

@BOOK{koniges00,
       EDITOR = "Alice E. Koniges",
       TITLE = "Industrial Strength Parallel Computing",
       PUBLISHER = "Morgan Kaufmann Publishers",
       address = "San Francisco",
       YEAR = 2000
}


@Misc{fftw-web-page,
  key = {Fftw},
  title =	 {{FFTW} {Web} page},
  note =	 {\texttt{http://www.fftw.org/}},
  annote =	 {fast FFT.  Parallel versions with MPI and Cilk}
}

@inproceedings{FrigoJohnson93,
  author    = {Matteo Frigo and Steven G. Johnson},
  title     = {The Design and Implementation of {FFTW3}},
  booktitle = {Proceedings of the IEEE},
  volume    = {93},
  number    = {2},
  pages     = {216--231},
  year      = {2005}
}

@BOOK{Kelley95,
      AUTHOR="C. T. Kelley",
      TITLE="Iterative Methods for Linear and Nonlinear Equations",
      YEAR="1995",
      PUBLISHER="SIAM",
      address="Philadelphia"
      }

@BOOK{NW99,
      AUTHOR="Jorge Nocedal and Stephen J. Wright",
      TITLE="Numerical Optimization",
      YEAR="1999",
      PUBLISHER="Springer-Verlag",
      address="New York"
      }

@book{szyperski98,
       AUTHOR = "Clemens Szyperski",
       TITLE = "Component Software: Beyond Object-Oriented Programming",
       PUBLISHER = "ACM Press",
       address = "New York",
       YEAR = 1998
}

@article{broy98,
  Author = "Manfred Broy and Anton Deimel and Juergen Henn and Kai Koskimies and
            Franti\v{s}ek Pl\'{a}\v{s}il and Gustave Pomberger and Wolfgang Pree and Michael Stal
            and Clemens Szyperski",
  Title = "What Characterizes a (Software) Component?" ,
  Journal = "Software -- Concepts and Tools",
  Publisher = "Springer-Verlag",
  Year= 1998,
  volume = 19,
  pages = "49-56"
}

@Unpublished{spai-web-page,
  title = 	 "{SPAI} {W}eb {P}age",
  note = 	"http://www.sam.math.ethz.ch/\~{ }grote/spai/",
  author      = "Steven Bernard and Marcus Grote",
  institution = "NASA Ames Research Center and ETH Zurich"
}

@article( gh97,
    Author  = "M. J. Grote and T. Huckle",
    Title   = "Parallel Preconditioning with Sparse Approximate Inverses",
    Year    = 1997,
    Journal = "SIAM J. of Scient. Comput.",
    Volume  = 18,
    pages   = "838-853"
    )
@article( zhang96,
    Author = "Wen Zhang",
    Title  = "Using {MOL} to Solve a high order nonlinear {PDE} with a moving
         boundary in the simulation of a sintering process",
    Year   = 1996,
    Journal = "Appl. Numer. Math.",
    Volume = 20,
    pages  = "235-244",
    )

@article( zhang98,
    Author = "Wen Zhang and Ian Gladwell",
    Title  = "The sintering of two particles by surface and grain boundary
         diffusion - a three-dimensional numerical study",
    Journal = "Comp. Mater. Sci.",
    year = 1998,
    volume = 12
    )

@inproceedings{MollerSchwartzbach01,
  AUTHOR = "Anders M\o{}ller and Michael I. Schwartzbach",
  TITLE = "The Pointer Assertion Logic Engine",
  BOOKTITLE = "ACM Proceedings of PLDI'01",
  YEAR = "2001",
}

@inproceedings{KlarlandSchwartzbach97,
  AUTHOR = "Nils Klarland and Michael I. Schwartzbach",
  TITLE = "A Domain-Specific Languages for Regular Sets of Strings and Trees",
  BOOKTITLE = "Proceedings of the Conference on Domain-Specific Languages",
  PUBLISHER = "USENIX",
  MONTH = "October",
  YEAR = "1997",
  ADDRESS = "Santa Barbara, CA",
}

@inproceedings{ConselMarlet98,
  AUTHOR = "C. Consel and R. Marlet",
  TITLE = "Architecturing software using a methodology for language development",
  BOOKTITLE = "Proceedings of the 10th International Symposium on Programming Languages, Implementations, Logics and Programs",
  YEAR = "1998",
  PAGES = "170-174",
  MONTH = "September",
  ADDRESS = "Pisa, Italy",
}

@misc{sundials:homepage,
   author = "C. {Woodward et al.}",
   title = "{SUNDIALS {W}eb page}",
   howpublished  = "\url{https://computation.llnl.gov/casc/sundials/main.html}"
}

@misc{sundials-user-ref,
  title       = "{SUNDIALS}: Suite of Nonlinear and Differential/Algebraic Equation Solvers",
  note        =	"See \url{http://www.llnl.gov/CASC/sundials}",
  author      = "Allan Hindmarsh and Peter Brown and Keith Grant and Steven Lee and Radu Serban and Dan Shumaker and Carol Woodward",
  institution = "Center for Applied Scientific Computing, Lawrence Livermore National Laboratory",
  number = "UCRL-JP-200037",
  year = 2003
}

@article{sundials05,
  author = "A. Hindmarsh and P. Brown and K. Grant and S. Lee and R. Serban and D. Shumaker and C. Woodward",
  title = "{SUNDIALS:} Suite of Nonlinear and Differential/Algebraic Equation Solvers",
  journal = "ACM Transactions on Mathematical Software",
  volume = 31,
  number = 3,
  pages = "363--396",
  year = 2005
}

@inproceedings{serban2005cvodes,
  title={{CVODES}, the sensitivity-enabled {ODE} solver in {SUNDIALS}},
  author={Serban, Radu and Hindmarsh, Alan C},
  booktitle={Proceedings of the 5th International Conference on Multibody Systems, Nonlinear Dynamics and Control, Long Beach, CA},
  year={2005}
}

@article{pvode99,
  author = "G. Byrne and A. Hindmarsh",
  title = "{PVODE}, An {ODE} Solver for Parallel Computers",
  journal = "Int. J. High Perf. Comput. Apps.",
  volume = 13,
  number = 4,
  year = 1999,
  pages = "354 -- 365"
}

@article{cvode95,
  author = "S. Cohen and A. Hindmarsh",
  title = "{CVODE}, A Stiff/Nonstiff {ODE} Solver in {C}",
  journal = "Computers in Physics",
  volume = 10,
  number = 2,
  year = 1996,
  pages = "138 -- 143"
}

@techreport{ifpack,
  title       = "Robust Algebraic Preconditioners using {IFPACK} 3.0",
  author      = "Marzio Sala and Michael Heroux",
  institution = "Sandia National Laboratories",
  number      = "SAND2005-0662",
  year = "2005"
}

@techreport{kinsol-user-ref,
  title       = "User Documentation for {KINSOL}, A Nonlinear Solver for Sequential and Parallel Computers",
  author      = "Allan Taylor and Alan Hindmarsh",
  institution = "Center for Applied Scientific Computing, Lawrence Livermore National Laboratory",
  number      = "UCRL-ID-131185",
  year = 1998
}

@article{FiardManteuffelMcCormick98,
  author  = "J.-M. Fiard and T. Manteuffel and S. McCormick",
  title   = "First-order system least squares {(FOSLS)} for convection-diffusion problems: numerical results",
  journal = "SIAM J. Sci. Comp.",
  year    = 1998,
  volume  = 19,
  pages   = {1958--1979}
}

@inproceedings{Vuduc02,
  AUTHOR = "Richard Vuduc and James W. Demmel and Katherine A. Yelick and Shoaib Kamil and Rajesh Nishtala and Benjamin Lee",
  TITLE = "Performance Optimizations and Bounds for Sparse Matrix-Vector Multiply",
  BOOKTITLE = "Proceedings of Supercomputing",
  YEAR = "2002",
  MONTH = "November",
  ADDRESS = "Baltimore"
}

@article{BeckerRannacher01,
  author  = "R. Becker and R. Rannacher",
  title   = "An optimal control approach to a posteriori error estimation in finite element methods",
  journal = "Acta Numerica",
  year    = "2001",
  volume  = "10",
  pages   = {1--102}
}

@article{BabuskaMiller84a,
  author  = "I. Babu$\check{s}$ka and A.D. Miller",
  title   = "The post-processing approach in the finite element method, {I}: Calculations of displacements, stresses, and
other higher derivatives of the displacements",
  journal = "Int. J. Numer. Meth. Eng.",
  year    = "1984",
  volume  = "20",
  pages   = {1085--1109}
}

@article{BabuskaMiller84b,
  author  = "I. Babu$\check{s}$ka and A.D. Miller",
  title   = "The post-processing approach in the finite element method, {II}: The calculation of stress intensity
factors",
  journal = "Int. J. Numer. Meth. Eng.",
  year    = "1984",
  volume  = "20",
  pages   = {1111--1129}
}

@article{BabuskaMiller84c,
  author  = "I. Babu$\check{s}$ka and A.D. Miller",
  title   = "The post-processing approach in the finite element method, {III}: A posteriori error estimation and adaptive
mesh refinement",
  journal = "Int. J. Numer. Meth. Eng.",
  year    = "1984",
  volume  = "20",
  pages   = {2311--2324}
}

@unpublished{jtb-web-page,
  title       = "{The Java Tree Builder}",
  note        =	"See \url{http://www.cs.purdue.edu/jtb}",
  author      = "Jens Palsberg",
  institution = "Purdue University"
}

@unpublished{Palsberg98,
  title       = "Why Visitors?",
  note        =	"See \url{http://www.cs.purdue.edu/jtb/whyvisitors}",
  author      = "Jens Palsberg",
  institution = "Purdue University",
  year        = "1998"
}

@unpublished{ply-web-page,
  title       = "{PLY (Python Lex-Yacc)}",
  note        =	"\url{http://systems.cs.chicago.edu/ply}",
  author      = "David Beazley",
  institution = "University of Chicago"
}

@misc{adic-web-page,
  title       = "{ADIC Web page}",
  note        =	"\url{http://www.mcs.anl.gov/autodiff}",
  author      = "Paul Hovland and Uwe Naumann and Boyana Norris",
  institution = "Argonne National Laboratory"
}

@article{Naumann02,
  author  = "Uwe Naumann",
  title   = "Optimal accumulation of {J}acobian matrices by elimination methods on the dual computational graph",
  journal = "Mathematical Programming (to appear)",
  note    = "Preprint ANL/MCS-P944-0402, Argonne National Laboratory, April 2002",
  year    = "2003"
}

@article{kaper1,
  author  = "H. G. Kaper and T. J. Kaper",
  title   = "Asymptotic Analysis of Two Reduction Methods for Systems of Chemical Reactions",
  journal = "Physica D",
  year    = "2002",
  pages   = "66--93",
  volume  = "165"
}

@misc{ veltisto-web-page,
  author =       "George Biros",
  title =        "{Veltisto Web page}",
  note =         "\url{http://www.cs.nyu.edu/~biros/veltisto}",
}

@article{KarypisKumar98,
  author  = "George Karypis and Vipin Kumar",
  title   = "A Parallel Algorithm for Multilevel Graph Partitioning and Sparse Matrix Ordering",
  journal = "Journal of Parallel and Distributed Computing",
  volume  = "48",
  pages   = "71--85",
  year    = "1998"
}

@techreport{KarypisKumar97,
	Author = {Karypis, George and Kumar, V.},
	Institution = {Department of Computer Science, University of Minnesota},
	Keywords = {graph partitioning; ParMetis},
	Note = {http://www.cs.umn.edu/~metis},
	Number = {97-060},
	Title = {{ParMETIS}: Parallel graph partitioning and sparse matrix ordering library},
	Year = {1997}
}

@misc{ parmetis-web-page,
  author =       "George {Karypis et al.}",
  title =        "{ParMETIS Web page}",
  note =         "\url{http://www.cs.umn.edu/~karypis/metis/parmetis}",
  year = "2005"
}

@misc{ sparskit-web-page,
  author =       "Yousef {Saad et al.}",
  title =        "{SPARSKIT Web page}",
  note =         "\url{http://www.cs.umn.edu/~saad/software/SPARSKIT/sparskit.html}",
}

@misc{ dscpack-web-page,
  author =       "Padma Raghavan",
  title =        "{DSCPACK Web page}",
  note =         "\url{http://www.cse.psu.edu/~raghavan/Dscpack}"
}

@Misc{ gaussian-web-page,
  author =       "",
  title =        "{Gaussian Web page}",
  note =         "\url{http://gaussian.com}",
  key =        "{Gaussian} {Web} page",
}

@Book{lapack-user-guide,
  author = 	 "E. Anderson and Z. Bai and C. Bischof and S. Blackford and J. Demmel and
                  J. Dongarra and J. Du Cris and A. Greenbaum and S. Hammarling and
                  A. McKenney and D. Sorensen",
  title = 	 "LAPACK Users' Guide, Third Edition",
  publisher = 	 "SIAM",
  year = 	 "1999"
}

@Manual{	  nwchem4.1,
  author        = {High Performance Computational Chemistry Group},
  title		= {{NWChem}, A Computational Chemistry Package for Parallel
		  Computers, Version 4.1},
  year		= 2002,
  organization	= {Pacific Northwest National Laboratory},
  address	= {Richland, Washington 99325-0999 USA},
  note          = {See \url{http://www.emsl.pnl.gov/pub/docs/nwchem/}},
}

@TechReport{tchem,
  title={{TC}hem: {A} Software Toolkit for the Analysis of Complex Kinetic Models},
  author={Cosmin Safta and Habib Najm and Omar Knio},
  institution = {Sandia National Laboratories},
  number = {SAND2011-3282},
  year=2011,
}
@Misc{ scidac-web-page,
  author =       "",
  title =        "{{SciDAC Initiative Web page}}",
  note =         "\url{http://www.osti.gov/scidac}",
  key =        "{SciDAC Initiative Web page}"
}

@Misc{cmrs:homepage,
  author =	 {Amitava {Bhattacharjee (PI)}},
  title =	 {{Center for Magnetic Reconnection Studies}},
  howpublished = {\url{http://www.physics.uiowa.edu/cmrs}}
}

@Misc{tops:homepage,
  author =	 {David {Keyes (PI)}},
  title =	 {{Towards Optimal Petascale Simulations (TOPS) Center}},
  howpublished = {\url{http://scalablesolvers.org}}
}

@Misc{tstt:homepage,
  author =	 {David Brown and Jim Glimm and Lori Freitag},
  title =	 {{Terascale Simulation Tools and Technology (TSTT) Center}},
  howpublished = {\url{http://www.tstt-scidac.org}},
  year = {2005}
}

@Misc{petsc:applications,
  author =	 {B. F. {Smith et al.}},
  title =	 {{Scientific Applications Using {PETSc}}},
  howpublished = {\url{http://www.mcs.anl.gov/petsc/publications}}
}

@Misc{petsc:users,
  author =	 {B. F. {Smith et al.}},
  title =	 {{PETSc User Statistics}},
  howpublished = {\url{http://www.mcs.anl.gov/petsc/miscellaneous/usage.html}}
}

@Misc{cemm:homepage,
  author =	 {Steve {Jardin (PI)}},
  title =	 {{Center for Extended MHD Modeling}},
  howpublished = {\url{http://w3.pppl.gov/CEMM}}
}

@Misc{m3d:homepage,
  author =	 {Steve {Jardin et al.}},
  title =	 {{M3D Web page}},
  howpublished = {\url{http://w3.pppl.gov/m3d}}
}

@Misc{nimrod:homepage,
  author =	 {Carl R. {Sovinec et al.}},
  title =	 {{NIMROD Web page}},
  howpublished = {http://nimrodteam.org}
}

@misc{grace-web-page,
   author = "Manish {Parashar et al.}",
   title = "{GrACE Web Page}",
   howpublished  = "\url{http://www.caip.rutgers.edu/~parashar/TASSL/Projects/GrACE}",
}

@misc{accel1,
   title = "Advanced Computing for 21st Century Accelerator Science and Technology Web page",
   howpublished  = "\url{http://scidac.nersc.gov/accelerator/}",
   author = "K. Ko and R. Ryne (PIs)"
}

@unpublished{KatzSpiegelman03,
  author  = "Richard F. Katz and Marc Spiegelman",
  title   = "A semi-{L}agrangian {C}rank-{N}icholson algorithm for the numerical solution of advection-diffusion problems",
  note    = "Columbia University, in preparation",
}

@misc{acts:homepage,
   author = "",
   title = "{Advanced CompuTational Software (ACTS) Web page}",
   howpublished  = "\url{http://acts.nersc.gov}",
   key = "{Advanced CompuTational Software (ACTS) Web page}",
}
@article{superlu99,
  author  = {James W. Demmel and Stanley C. Eisenstat and John R. Gilbert and Xiaoye S. Li and Joseph W. H. Liu},
  title = {A supernodal approach to sparse partial pivoting},
  journal = {SIAM J. Matrix Analysis and Applications},
  year = {1999},
  volume  = {20},
  number = {3},
  pages = {720-755}
}
@misc{superlu:homepage,
   author = "J. Demmel and J. Gilbert and X. Li",
   title = "{SuperLU Web page}",
   howpublished  = "http://crd.lbl.gov/\~xiaoye/SuperLU"
}

@inproceedings{ccf98,
 author=     "E. Chow and A. Cleary and R. Falgout",
 title=      "Design of the hypre Preconditioner Library",
 booktitle = "Proceedings of the SIAM Workshop on Object Oriented Methods for
              Inter-operable Scientific and Engineering Computing",
 publisher = "SIAM",
 year=       1999,
}


@TechReport{hypre-users-manual,
  author      = "R. Falgout",
  title       = "{hypre} Users Manual",
  number      = "Revision 2.11.2",
  institution = "Lawrence Livermore National Laboratory",
  year        = 2017
}


@misc{hypre:homepage,
   author = "R. Falgout",
   title = "{hypre Web page}",
   howpublished  = "\url{http://www.llnl.gov/CASC/hypre}"
}

@InProceedings{trilinos:gpu,
  author =	 {C.G. Baker and  M.A. Heroux. and H.C. Edwards and  A.B. Williams},
  title =	 {A Light-weight API for Portable Multicore Programming},
  booktitle =	 {18th Euromicro International Conference on Parallel, Distributed and Network-Based Processing (PDP)},
  pages =	 {601--606},
  publisher =	 {IEEE},
  year =	 {2010}
}

@inproceedings{heroux2004design,
  title={The design of {T}rilinos},
  author={Heroux, Michael A and Sala, Marzio},
  booktitle={International Workshop on Applied Parallel Computing},
  pages={620--628},
  year={2004},
  organization={Springer}
}

@misc{trilinos:homepage,
   author = "M. {Heroux et al.}",
   title = "{Trilinos Web page}",
   howpublished  = "{\tt http://trilinos.sandia.gov/}"
}

@article{trilinos:overview,
author = {Michael A. Heroux and Roscoe A. Bartlett and Vicki E. Howle and Robert J. Hoekstra and Jonathan J. Hu and Tamara G. Kolda and Richard B. Lehoucq and Kevin R. Long
          and Roger P. Pawlowski and Eric T. Phipps and Andrew G. Salinger and Heidi K. Thornquist and Ray S. Tuminaro and James M. Willenbring and Alan Williams and Kendall S. Stanley},
title = {An overview of the {T}rilinos project},
journal = {ACM Transactions on Mathematical Software},
volume = {31},
number = {3},
year = {2005},
issn = {0098-3500},
pages = {397--423},
publisher = {ACM Press}
}
%doi = {http://doi.acm.org/10.1145/1089014.1089021},

@misc{rythmos:homepage,
  author = "T. Coffey and R. Bartlett",
  title = "Rythmos: Transient Integration of Differential Equations",
  howpublished = "\url{http://trilinos.sandia.gov/packages/rythmos}"
}

@misc{triangle:homepage,
   author = "J. {Shewchuk}",
   title = "{Triangle: A Two-Dimensional Quality Mesh Generator and Delaunay Triangulator}",
   howpublished  = "\url{http://www-2.cs.cmu.edu/~quake/triangle.html}",
   year = "2005"
}

@misc{tetgen:homepage,
   author = "Hang {Si}",
   title = "{TetGen: A Quality Tetrahedral Mesh Generator and Three-Dimensional Delaunay Triangulator}",
   howpublished  = "\url{http://tetgen.berlios.de}",
   year = "2005"
}

@misc{eigen:homepage,
  author = {Benoit Jacob and Ga\"el Guennebaud},
  title  = {{Eigen} {W}eb page},
  key    = {Jacob},
  url    = {http://eigen.tuxfamily.org/},
  howpublished = {\url{http://eigen.tuxfamily.org/}},
  year   = {2015}
}

@misc{dune:homepage,
  author = {Peter Bastian and Markus Blatt and Andreas Dedner and Christian Engwer and Jorrit Fahlke and Christoph Gersbacher and Carsten Gr\"aser and Christoph Gr\"uninger Robert Kl\"ofkorn and Steffen M\"uthing and Martin Nolte and Mario Ohlberger and Oliver Sander},
  title  = {{DUNE} {W}eb page},
  key    = {Bastian},
  url    = {http://www.dune-project.org/},
  howpublished = {\url{http://www.dune-project.org/}},
  year   = {2015}
}

@misc{thrust,
   author = "N. Bell and J. Hoberock",
   title = {The {T}hrust Library},
   howpublished  = "{\tt http://code.google.com/p/thrust/}",
   year = "2010"
}

@misc{cusp,
   author = "N. Bell and M. Garland",
   title = {The {C}usp Library},
   howpublished  = "{\tt http://code.google.com/p/cusp-library/}",
   year = "2010"
}

@misc{CIG:homepage,
   author = "M. {Gurnis et al.}",
   title = "{Computational Infrastructure for Geodynamics}",
   howpublished  = "\url{http://www.geodynamics.org}"
}

@article{MaltsevSelkov00,
  author  = "R. Overbeek and N. Larsen and G. Pusch and M. D'Souza and E. Selkov Jr. and N. Kyrpides and M. Fonstein and N. Maltsev and E. Selkov",
  title   = "{WIT}: {I}ntegrated system for high-throughput genome sequence analysis and metabolic reconstruction",
  journal = "Nucleic Acids Res.",
  year    = "2000",
  month   = "January",
  pages   = "123-125",
  volume  = "28",
  number  = "1",
}

@article{more:coloring,
  author  = "Thomas F. Coleman and Jorge J. Mor\'{e}",
  title   = "Estimation of sparse {J}acobian matrices and graph coloring problems",
  journal = "SIAM Journal on Numerical Analysis",
  year    = "1983",
  month   = "Feb.",
  pages   = "187--209",
  volume  = "20",
  number  = "1",
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@article{SelkovMaltsev97,
  author  = "E. Selkov and N. Maltsev and G.J. Olsen and R. Overbeek and W. B. Whitman",
  title   = "A reconstruction of the metabolism of Methanococcus jannaschii from sequence data",
  journal = "Gene",
  year    = "1997",
  pages   = "GC11-GC26",
  volume  = "197",
  number  = "1-2",
}

@unpublished{rocketcenter,
  title       = "Center for Simulation of Advanced Rockets",
  note        =	"http://www.csar.uiuc.edu",
  institution = "University of Illinois at Urbana-Champaign"
}

@article{Kirby03,
  title       = {A posteriori error estimates for the mixed hybrid finite element method},
  author      = {Robert C Kirby},
  journal     = {Computational Geosciences},
  volume      = {7},
  pages       = {197--214},
  note        =	{\url{http://www.ices.utexas.edu/~clint/nsf/apostmfem.ps}},
  year        = {2003},
}

@article{Kirby2003B,
  title   = {On the convergence of high resolution methods with multiple time scales for hyperbolic conservation laws},
  author  = {Robert C Kirby},
  journal = {Mathematics of computation},
  volume  = {72},
  number  = {243},
  pages   = {1239--1250},
  year    = {2003}
}

@article{DawsonKirby2001,
  title   = {High resolution schemes for conservation laws with locally varying time steps},
  author  = {Clint Dawson and Robert C Kirby},
  journal = {SIAM Journal on Scientific Computing},
  volume  = {22},
  number  = {6},
  pages   = {2256--2281},
  year    = {2001},
  publisher = {SIAM}
}

@article{DawsonKirby1999,
  title   = {Solution of parabolic equations by backward Euler-mixed finite element methods on a dynamically changing mesh},
  author  = {Clint Dawson and Robert C Kirby},
  journal = {SIAM Journal on Numerical Analysis},
  volume  = {37},
  number  = {2},
  pages   = {423--442},
  year    = {1999},
  publisher = {SIAM}
}

@article{BarthLarson00,
  author  = "T. J. Barth and M. G. Larson",
  title   = "{\em A posteriori} Error Estimation for Discontiuous {G}alerkin Approximations of Hyperbolic Systems",
  journal = "LNCS",
  year    = "2000",
  volume  = "11",
  publisher = "Spinger-Verlag",
}

@Article{xu1,
  author    = "J. Xu",
  title     = "Iterative Methods by Space Decomposition and Subspace Correction",
  journal =   "SIAM Review",
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  year      = 1992
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@Article{Brandt77,
  author  = "Achi Brandt",
  title   = "Multi-Level Adaptive Solutions to Boundary-Value Problems",
  journal = "Mathematics of Computation",
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  pages   = "333--390",
  volume  = "31",
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@article{brandt1979multigrid,
  title={{Multigrid solutions to elliptic flow problems}},
  author={Brandt, A. and Dinar, N.},
  journal={Numerical Methods for Partial Differential Equations},
  pages={53--147},
  year={1979}
}

@incollection{brandt1979singular,
  title={Multi-Level Adaptive Techniques(MLAT) for singular-perturbation problems},
  author={Achi Brandt},
  booktitle={Numerical Analysis of Singular Perturbation Problems},
  editor={Hemker, Pieter W. and Miller, John J.H.},
  pages={53--142},
  year={1979},
  publisher={Academic Press}
}

@Article{amge1,
  author    = "M. Brezina and A. J. Cleary and R. D. Falgout and V. E. Henson and J. E. Jones and T. A. Manteuffel and
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  title     = "Algebraic Multigrid Based on Element Interpolation (AMGe)",
  journal =   "SIAM J. Scientific Computing",
  volume = "22",
  pages = "1570--1592",
  year      = 2000
}

@BOOK{bramble1,
       AUTHOR = "J. H. Bramble",
       TITLE = "Multigrid Methods",
       PUBLISHER = "Longman Scientific and Technical",
       address = "Essex, England",
       YEAR = 1993
}

@BOOK{arpack98,
       AUTHOR = "R. B. Lehoucq and D. C. Sorensen and C. Yang",
       TITLE = "ARPACK, Users' Guide",
       PUBLISHER = "SIAM",
       YEAR = 1998
}

@Article{bbder96,
  author    = "R. Barrett and M.  Berry and J. Dongarra and V. Eijkhout and C. Romine",
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  year      = "1996",
  volume    = "74",
  pages     = "91--110"
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@Article{egks94,
  author    = "A. Ern and V. Giovangigli and D. E. Keyes and M. D. Smooke",
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  journal =   "SIAM J. Scientific Computing",
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@Article{dftb02,
  author    = "P. Zapol and M. Sternberg and L.A. Curtiss and Th. Frauenheim and D.M. Gruen",
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@INBOOK{lsa,
        AUTHOR="R. Bramley and D. Gannon and T. Stuckey and J. Villacis and
        J. Balasubramanian and  E. Akman and F.  Berg and  S.  Diwan and M.  Govindaraju",
        TITLE="The linear system analyzer",
        SERIES="enabling technologies for computational science",
        YEAR="2002",
        PUBLISHER="Kluwer",
        LOCATION="Dordrecht"
     }

@Article{kk97,
  author    = "Carl T. Kelley and David E. Keyes",
  title     = "Convergence analysis of pseudo-transient continuation",
  journal =   "SIAM J. Numerical Analysis",
  year      = "1998",
  volume    = "35",
  pages     = "508--523"
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@Article{swtm01,
  author =        "R. Shepard and A. F. Wagner and J. L. Tilson and M. Minkoff",
  journal =      "Journal of Computational Physics",
  year = "2001",
  volume = "172",
  number = "2",
  pages = "472--514",
  title  =  "The Subspace Projected Approximate Matrix {(SPAM)} Modification of the {D}avidson Method"
}

@techreport{ zhou03,
  author =       "Y. Zhou",
  title =        "Eigenvalue Computation from the Optimization Perspective: On {Jacobi-Davidson,
                  IIGD, RQI and Newton} Updates",
  institution =  "Argonne National Laboratory",
  number =       "ANL/MCS-P1074-0803",
  note =         "Submitted to Numerical Linear Algebra with Applications",
  year = 2003
}

@Unpublished{ mtwm03,
  author =       "G. G. Maisuradze and D. L. Thompson and A. F. Wagner and M. Minkoff",
  title =        "Interpolating moving least squares methods for fitting
                  potential energy surfaces:  Detailed analysis of one-dimensional applications",
  note =         "to appear in the Journal of Chemical Physics",
  year = 2003
}

@article{SinghJosephHeslaGlowinskiPan00,
  author  = "P. Singh and D. D. Joseph and T. Hesla and R. Glowinski and T.-W. Pan",
  title   = "A distributed {L}agrange multiplier/fictitious domain model for viscoelastic particulate flows",
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@Misc{triangle-web-page,
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@article{leaf3,
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@article{leaf4,
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@article{leaf5,
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@article{GraySumpterNoidBarnes01,
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@InProceedings{petsc-efficient,
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@article{MUMPS01,
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@article{Zoltan06,
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@article{lidemmel03,
     AUTHOR = {Xiaoye S. Li and James W. Demmel},
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@TechReport{SuperLU,
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@techreport{Trilinos-Overview03,
title = "{An Overview of {T}rilinos}",
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@unpublished{facets:homepage,
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@unpublished{cpes:homepage,
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@BOOK{hazeltine-meiss-book,
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@unpublished{compass:homepage,
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@misc{unic-ref,
  author = "Giuseppe Palmiotti",
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% -----------------------------------------------------------------------
% Model coupling refs

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@Misc{csafe:web,
  author = "D. {Pershing (Director)}",
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}

@Misc{cits:web,
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@Misc{flash:web,
  author = "D. {Lamb (Director)}",
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@techreport{utah-csafe03,
  author = "J. Guilkey and T. Harman and A. Xia and B. Kashiwa and P. McMurtry",
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@INPROCEEDINGS{cactus02,
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@misc{cactus:homepage,
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@Misc{open-grid-forum:web,
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@techreport{drashansky96,
  title = "Multidisciplinary Problem Solving using Agents in a Cluster Environment",
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@article{michopoulos05,
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@article{dubey09,
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@Book{BottLoring95,
  AUTHOR    = "Raoul Bott and Loring W. Tu",
  TITLE	    = "Differential Forms in Algebraic Topology",
  PUBLISHER = "Springer",
  YEAR	    = "1995"
}

@Book{KobayashiNomizu96,
  AUTHOR    = "Shoshichi Kobayashi and Katsumi Nomizu",
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  YEAR	    = "1996"
}

@Article{HornungKohn02,
  author  = {Richard D. Hornung and Scott R. Kohn},
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@inproceedings{concepts06,
  author    = "Douglas Gregor and Jaakko J{\"a}rvi and Jeremy Siek and Bjarne Stroustrup and Gabriel Dos Reis and Andrew Lumsdaine",
  title     = "Concepts: Linguistic Support for Generic Programming in C++",
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@BOOK{Hatcher02,
  AUTHOR = {Hatcher, Allen},
  TITLE = {Algebraic Topology},
  PUBLISHER = {Cambridge University Press},
  YEAR = 2002
}

@book{GammaHelmJohnsonVlissides95,
	abstract = {{Design Patterns is a modern classic in the literature of object-oriented development, offering timeless and elegant solutions to common problems in software design. It describes patterns for managing object creation, composing objects into larger structures, and coordinating control flow between objects. The book provides numerous examples where using composition rather than inheritance can improve the reusability and flexibility of code. Note, though, that it's not a tutorial but a catalog that you can use to find an object-oriented design pattern that's appropriate for the needs of your particular application--a selection for virtuoso programmers who appreciate (or require) consistent, well-engineered object-oriented designs.} {Now on CD, this internationally acclaimed bestseller is more valuable than ever!

Use the contents of the CD to create your own design documents and reusable components. The CD contains: 23 patterns you can cut and paste into your own design documents; sample code demonstrating pattern implementation; complete Design Patterns content in standard HTML format, with numerous hyperlinked cross-references; accessed through a standard web browser; Java-based dynamic search mechanism, enhancing online seach capabilities; graphical user environment, allowing ease of navigation.

First published in 1995, this landmark work on object-oriented software design presents a catalog of simple and succinct solutions to common design problems. Created by four experienced designers, the 23 patterns contained herein have become an essential resource for anyone developing reusable object-oriented software. In response to reader demand, the complete text and pattern catalog are now available on CD-ROM. This electronic version of Design Patterns enables programmers to install the book directly onto a computer or network for use as an online reference for creating reusable object-oriented software.

The authors first describe what patterns are and how they can help you in the design process. They then systematically name, explain, evaluate, and catalog recurring designs in object-oriented systems. All patterns are compiled from real-world examples and include code that demonstrates how they may be implemented in object-oriented programming languages such as C++ and Smalltalk. Readers who already own the book will want the CD to take advantage of its dynamic search mechanism and ready-to-install patterns.}},
  author = {Gamma, Erich and Helm, Richard and Johnson, Ralph and Vlissides, John},
  citeulike-article-id = {115158},
  howpublished = {Hardcover},
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  keywords = {1995 algorithms architecture book books computer computing design design-pattern design-patterns design_patterns designpatterns development diplom entwurfsmuster four gang gof java mathgamespatterns no-tag object object-orientation object-oriented of oo-patterns oop oriented pattern patterns programming se software software-development software-engineering software_design softwareengineering standard},
  month = {January},
  publisher = {{Addison-Wesley Professional}},
  title = {Design Patterns},
  url = {http://www.amazon.ca/exec/obidos/redirect?tag=citeulike04-20{\&}path=ASIN/0201633612},
  year = {1995}
}

@inproceedings{Chaco95,
 author = {Bruce Hendrickson and Robert Leland},
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 year = {1995},
 isbn = {0-89791-816-9},
 pages = {28},
 location = {San Diego, California, United States},
 doi = {http://doi.acm.org/10.1145/224170.224228},
 publisher = {ACM Press},
 address = {New York},
}

@BOOK{Aleksandrov98,
  AUTHOR = {Aleksandrov, Pavel S.},
  TITLE = {Combinatorial Topology},
  PUBLISHER = {Dover},
  VOLUME = 3,
  YEAR = 1998
}

@book{Steenrod99,
	abstract = {{
Fibre bundles, now an integral part of differential geometry, are also of great importance in modern physics--such as in gauge theory. This book, a succinct introduction to the subject by renown mathematician Norman Steenrod, was the first to present the subject systematically.

It begins with a general introduction to bundles, including such topics as differentiable manifolds and covering spaces. The author then provides brief surveys of advanced topics, such as homotopy theory and cohomology theory, before using them to study further properties of fibre bundles. The result is a classic and timeless work of great utility that will appeal to serious mathematicians and theoretical physicists alike.
}},
	author = {Steenrod, Norman},
	citeulike-article-id = {712999},
	howpublished = {Paperback},
	isbn = {0691005486},
	keywords = {fibre_bundles topology},
	month = {April},
	publisher = {{Princeton University Press}},
	title = {The Topology of Fibre Bundles. (PMS-14)},
	url = {http://www.amazon.ca/exec/obidos/redirect?tag=citeulike04-20{\&}path=ASIN/0691005486},
	year = {1999}
}

@BOOK{Bredon97,
  AUTHOR = {Bredon, Glen E.},
  TITLE = {Sheaf Theory},
  PUBLISHER = {Springer},
  PAGES = {524},
  SERIES = {Graduate Texts in Mathematics},
  YEAR = 1997
}

@techreport{TautgesMeyers04,
  title       = "{MOAB}: A Mesh-Oriented Database",
  author      = "Timothy J. Tautges and Ray Meyers and Karl Merkley and Clint Stimpson and Corey Ernst",
  institution = "Sandia National Laboratories",
  number      = "SAND2004-1592",
  month       = "April",
  year        = "2004"
}

@article{Tautges04,
  author  = {Timothy J. Tautges},
  title   = {{MOAB}-{SD}: Integrated Structured and Unstructured Mesh Representation},
  journal = {Engineering With Computers},
  volume  = {20},
  pages   = {286--293},
  year    = {2004}
}

@inproceedings{Meyers02,
  author    = {Ray Meyers et. al},
  title     = {{SNL} Implementation of the {TSTT} Mesh Interface},
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  month     = {June},
  year      = {2002}
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@inproceedings{SeolShepard05,
  author    = {E. S. Seol and Mark S. Shephard},
  title     = {A Flexible Distributed Mesh Data Structure to Support Parallel Adaptive Analysis},
  booktitle = {Proceedings of the 8th US National Congress on Computational Mechanics},
  year      = {2005},
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@article{BeallWalshShephard04,
  author  = {Mark W. Beall and Joe Walsh and Mark S. Shephard},
  title   = {A comparison of techniques for geometry access related to mesh generation},
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  year    = {2004}
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@article{CareyAndersonCarnesKirk04,
  author  = {Graham F. Carey and Michael L. Anderson and Brian R. Carnes and Benjamin S. Kirk},
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  journal = {Journal of Computational Applied Mathematics},
  volume  = {166},
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  pages   = {55--86},
  year    = {2004}
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@PHDTHESIS{GrALThesis,
  author = "Guntram Berti",
  title  = "Generic Software Components for Scientific Computing",
  school = "TU Cottbus",
  year   = "2000",
  note   = "\url{http://www.math.tu-cottbus.de/~berti/diss}"
}

@article{BeylkinCoifmanRokhlin91,
  author  = {Gregory Beylkin and Ronald Coifman and Vladimir Rokhlin},
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  year    = {1991}
}

@book{Wesseling92,
  author    = {Pieter Wesseling},
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@book{Grakakos04,
  author    = {Loukas Grakakos},
  title     = {Classical and Modern Fourier Analysis},
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  address   = {New Jersey},
  year      = {2004},
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@Misc{hlib-web-page,
  key    = {HLib},
  title  = {{HLib} {Web} page},
  note   = {{\texttt{http://www.hlib.org/}}},
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}

@article{Hackbusch99,
  author  = {Wolfgang Hackbusch},
  title   = {A sparse matrix arithmetic based on {$\mathcal H$}-matrices. Part {I}: Introduction to {$\mathcal H$}-matrices},
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@techreport{kay1999green,
  title={A {G}reen's function preconditioner for the steady-state {N}avier-{S}tokes equations},
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  institution={Oxford University Computing Laboratory},
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}
@article{bebendorf2003existence,
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  year={2003},
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@article{hackbusch2005direct,
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@techreport{DupHof2003,
  author      = {T. Dupont and J. Hoffman and C. Johnson and R. C. Kirby and M. G. Larson and A. Logg and L. R. Scott},
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  institution = {Chalmers Finite Element Center Preprint Series},
  number      = {2003--21},
  year        = {2003}
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@article{FLAME01,
  author  = {John A. Gunnels and Fred G. Gustavson and Greg M. Henry and Robert A. van de Geijn},
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  year    = {2001},
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@article{Puschel05,
  author  = {Markus P{\"u}schel and Jos{\'e} M. F. Moura and Jeremy Johnson and
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    Franz Franchetti and Aca Ga\v{c}i\'{c} and Yevgen Voronenko and Kang Chen
    and Robert W. Johnson and Nick Rizzolo},
  title   = {{SPIRAL}: Code Generation for {DSP} Transforms},
  journal = {Proceedings of the IEEE},
  volume  = {93},
  number  = {2},
  year    = {2005},
  note    = {special issue on "Program Generation, Optimization, and Adaptation"}
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@article{KirbyLogg06,
  author    = {Robert C. Kirby and Anders Logg},
  title     = {A compiler for variational forms},
  journal   = {ACM Transactions on Mathematical Software},
  volume    = {32},
  number    = {3},
  year      = {2006},
  issn      = {0098-3500},
  pages     = {417--444},
  doi       = {http://doi.acm.org/10.1145/1163641.1163644},
  publisher = {ACM Press},
  address   = {New York, NY},
}

@article{KirbyLogg07,
  author    = {Robert C. Kirby and Anders Logg},
  title     = {Efficient compilation of a class of variational forms},
  journal   = {ACM Transactions on Mathematical Software},
  volume    = {33},
  number    = {3},
  year      = {2007},
  issn      = {0098-3500},
  pages     = {17},
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  publisher = {ACM Press},
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@article{BankDupont81,
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@techreport{Adams00,
  author      = {Mark F. Adams},
  title       = {Evaluation of three unstructured multigrid methods on 3D finite element problems in solid mechanics},
  institution = {UC Berkeley},
  number      = {CSD-00-1103},
  year        = {2000},
  url         = {citeseer.ist.psu.edu/article/adams00evaluation.html}
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@article{BergenGradlHuelsemannRuede06,
  author  = {Benjamin Bergen and Tobias Gradl and Frank H\"ulsemann and Ulrich R\"ude},
  title   = {A Massively Parallel Multigrid Method for Finite Elements},
  journal = {Computing in Science \& Engineering},
  volume  = {8},
  number  = {6},
  pages   = {56--62},
  year    = {2006}
}

@MastersThesis{BruneThesis08,
    author  = {Peter R. Brune},
    title   = {Enabling Unstructured Multigrid Under the Sieve Framework},
    school  = {University of Chicago},
    address = {Chicago, IL},
    year    = {2008},
    month   = {February}
}

@article{ArnoldWinther02,
  author  = {Douglas N. Arnold and Ragnar Winther},
  title   = {Mixed finite elements for elasticity},
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  number  = {3},
  month   = {September},
  year    = {2002},
  pages   = {401--419},
  note    = {DOI:10.1007/s002110100348}
}

@article{ArnoldFalkWinther06,
  author    = {Douglas N. Arnold and Richard S. Falk and Ragnar Winther},
  title     = {Finite element exterior calculus, homological techniques, and applications},
  journal   = {Acta Numerica},
  year      = {2006},
  volume    = {15},
  pages     = {1--155},
  publisher = {Cambridge University Press},
  note      = {doi:10.1017/S0962492906210018}
}

@article{Kirby04,
  author    = {Robert C. Kirby},
  title     = {Algorithm 839: {FIAT}, a new paradigm for computing finite element basis functions},
  journal   = {ACM Transactions on Mathematical Software},
  volume    = {30},
  number    = {4},
  year      = {2004},
  issn      = {0098-3500},
  pages     = {502--516},
  doi       = {http://doi.acm.org/10.1145/1039813.1039820},
  publisher = {ACM Press},
  address   = {New York, NY},
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@article{Kirby06,
  author    = {Robert C. Kirby},
  title     = {Optimizing {FIAT} with level 3 {BLAS}},
  journal   = {ACM Transactions on Mathematical Software},
  volume    = {32},
  number    = {2},
  year      = {2006},
  issn      = {0098-3500},
  pages     = {223--235},
  doi       = {http://doi.acm.org/10.1145/1141885.1141889},
  publisher = {ACM Press},
  address   = {New York, NY},
}

@misc{BlueCrystal08,
  author = {{B}lue {C}rystal Cluster},
  title  = {Advanced {C}omputing {R}esearch {C}entre{,} {University of Bristol}},
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@article{Beylkin95,
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@inproceedings{Riehl08,
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  year      = {2008},
}

@article{Appel85,
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@ARTICLE{Ewald21,
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}

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@article{GreengardRokhlin97,
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@article{LuChengHuangMcCammon06,
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@misc{KritzKeyesFSP07,
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@misc{Crosscutting10,
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@misc{MonizRosner09,
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@misc{Blanford08,
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@misc{Exascale07,
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@misc{ASCRBreakthroughs08,
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@misc{petsc-RD100-2009,
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@article{newman09,
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@misc{www:fenics,
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@phdthesis{Rankin99,
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@inproceedings{WarrenSalmon93,
	Abstract = {We report on an efficient adaptive N-body method which we have recently designed and implemented. The algorithm computes the forces on an arbitrary distribution of bodies in a time which scales as N log N with the particle number. The accuracy of the force calculations is analytically bounded, and can be adjusted via a user defined parameter between a few percent relative accuracy, down to machine arithmetic accuracy. Instead of using pointers to indicate the topology of the tree, we identify...},
	Address = {New York},
	Author = {Warren, Michael S. and Salmon, John K.},
	Booktitle = {Proceedings of the 1993 ACM/IEEE Conference on Supercomputing},
	Citeulike-Article-Id = {580952},
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@unpublished{CruzWCCM10,
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  year   = {2010}
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@article{McGuffee06,
  author  = {S.~R. {McGuffee} and A.~H. Elcock},
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@ARTICLE{NilsenCaiHoylandLangtangen10,
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 keywords = {Computer Science - Distributed, Parallel, and Cluster Computing, Computer Science - Programming Languages},
     year = 2010,
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@misc{mcinnes:siam09:minisymposium,
  title = "Implicit Nonlinear Solvers in Multimodel Simulations",
  author = "L. C. McInnes and C. {Woodward (co-organizers)}",
  note = "invited minisymposium session at the SIAM Annual Meeting, July 9-10, 2009, Denver, CO,
speakers were: C. Woodward (LLNL), E. Myra (Univ. of Michigan), J. White (Stanford Univ.), A. Barker (Univ. of Colorado, Boulder), L. Wilcox (Univ. of Texas at Austin), R. Mills (ORNL), B. F. Smith (ANL), J. Shadid (SNL), D. Knoll (INL), G. Hansen (INL), J. Cary (Tech-X Corp.), T. Wildey (Univ. of Texas at Austin)."
}

@misc{mcinnes:fsp-summary:feb2011,
 author = "Lois Curfman McInnes and Luis Chacon and John Shadid",
 title = "Solvers and Time Integration Breakout Summary",
 note = "FSP Planning Workshop, General Atomics, Feb 8-11, 2011,
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}

@misc{dvi-materials:siamcse11,
   title = "Progress in Large-Scale Differential Variational Inequalities for Heterogeneous Materials",
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}

@misc{jamroz:cemm10,
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@misc{kruger:feb4-2011,
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@article{wright2001large,
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@misc{wright2002eigtool,
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@misc{visit-web-site,
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@book{Trefethen1996,
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@book{trefethen2005spectra,
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@article{gomez2010isogeometric,
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@Misc{fastmath:project,
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@Misc{exascale-software:proposal,
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@Misc{imex:project,
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@Misc{intel-mic:website,
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@Article{dudson:2009,
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title     = {{{BOUT++:}} a framework for parallel plasma fluid simulations},
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year      = 2009}

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@article{StubenAMG,
 author = {K. St\"{u}ben},
 title = {A review of algebraic multigrid},
 journal = {J. Comput. Appl. Math.},
 volume = {128},
 number = {1-2},
 year = {2001},
 issn = {0377-0427},
 pages = {281--309},
 doi = {http://dx.doi.org/10.1016/S0377-0427(00)00516-1},
 publisher = {Elsevier Science Publishers B. V.},
 address = {Amsterdam, The Netherlands, The Netherlands},
 }

@article{FeuchterMG,
author = "D. Feuchter and I. Heppner and S. Sauter and G. Wittum",
title = "Bridging the gap between geometric and algebraic multigrid methods",
journal = "Computing and visualization in science",
publisher = "Springer",
volume = "6",
number = "1",
year = "2003",
pages = "1--13",
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@article{ChowMGSmoothness,
    abstract = {For non-M-matrices, this paper proposes an unstructured multigrid method that only  attempts to interpolate in the directions of geometrical smoothness. These directions are  determined by analyzing samples of algebraically smooth error, e. Neighboring grid points i  and j are called smoothly coupled if e i and e j are consistently nearby in value. In addition,  these dierences may be used to dene interpolation weights. These new ideas may be  incorporated into the algebraic multigrid method. Test results show that the new method  can have much lower grid and operator complexities compared to AMG, leading to lower  solve timings.  1 },
    author = {Chow, Edmond},
    citeulike-article-id = {7675372},
    citeulike-linkout-0 = {http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.22.4305},
    journal = {American Journal of Mathematics},
    keywords = {fem, multigrid},
    pages = {197--215},
    posted-at = {2010-08-17 23:29:51},
    priority = {2},
    title = {An Unstructured Multigrid Method Based on Geometric Smoothness},
    url = {http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.22.4305},
    volume = {65},
    year = {2001}
}

@article{JonesAMGe,
    abstract = {{This paper contains the main ideas for an AMGe (algebraic multigrid for finite elements) method based on element agglomeration. In the method, coarse grid elements are formed by agglomerating fine grid elements. Compatible interpolation operators are constructed which yield coarse grid basis functions with a minimal energy property. Heuristics based on interpolation quality measures are used to guide the agglomeration procedure. The performance of the resulting method is demonstrated in two-level numerical experiments.}},
    author = {Jones, Jim E. and Vassilevski, Panayot S.},
    citeulike-article-id = {8598569},
    citeulike-linkout-0 = {http://scitation.aip.org/getabs/servlet/GetabsServlet?prog=normal&id=SJOCE3000023000001000109000001&idtype=cvips&gifs=yes},
    citeulike-linkout-1 = {http://link.aip.org/link/?SCE/23/109},
    journal = {SIAM Journal on Scientific Computing},
    keywords = {amg, fem, multigrid},
    number = {1},
    pages = {109--133},
    posted-at = {2011-01-13 18:05:55},
    priority = {2},
    publisher = {SIAM},
    title = {{AMGE Based on Element Agglomeration}},
    url = {http://scitation.aip.org/getabs/servlet/GetabsServlet?prog=normal&id=SJOCE3000023000001000109000001&idtype=cvips&gifs=yes},
    volume = {23},
    year = {2001}
}

@article{Saad1993,
author = {Saad, Youcef},
doi = {10.1137/0914028},
issn = {10648275},
journal = {SIAM Journal on Scientific Computing},
keywords = {65f10,ams,especially since the popularization,gate gradient,general purpose iterative methods,gmres,krylov subspace methods,mos,non-hermitian systems,of precondition-,preconditioned conju-,subject classi cations,variable preconditioners},
number = {2},
pages = {461--469},
title = {{A flexible inner-outer preconditioned GMRES algorithm}},
url = {http://dx.doi.org/10.1137/0914028},
volume = {14},
year = {1993}
}

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             Tobin Isaac and Xiangmin Jiao and Kirk Jordan and Dinesh Kaushik and
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 abstract = {We consider multiphysics applications from algorithmic and
architectural perspectives, where ``algorithmic'' includes both
mathematical analysis and computational complexity and
``architectural'' includes both software and hardware environments.
Many diverse multiphysics applications can be reduced, en route to
their computational simulation, to a common algebraic coupling
paradigm. Mathematical analysis of multiphysics coupling in this form
is not always practical for realistic applications, but model problems
representative of applications discussed herein can provide insight.
A variety of software frameworks for multiphysics applications have
been constructed and refined within disciplinary communities and
executed on leading-edge computer systems.  We examine several of
these, expose some commonalities among them, and attempt to
extrapolate best practices to future systems. From our study, we
summarize challenges and forecast opportunities.}
}

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@TechReport{ml-guide,
  author      =  {M.W. Gee and C.M. Siefert and J.J. Hu and R.S. Tuminaro and M.G. Sala},
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@article{Olson10,
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  pdf = {./files/2010_OlScTu_evosoc.pdf}
}

@article{Olson11,
 author = {Olson, Luke N. and Schroder, Jacob B. and Tuminaro, Raymond S.},
 title = {A General Interpolation Strategy for Algebraic Multigrid Using Energy Minimization},
 journal = {SIAM J. Sci. Comput.},
 issue_date = {April 2011},
 volume = {33},
 issue = {2},
 month = apr,
 year = {2011},
 issn = {1064-8275},
 pages = {966--991},
 numpages = {26},
 url = {http://dx.doi.org/10.1137/100803031},
 doi = {http://dx.doi.org/10.1137/100803031},
 acmid = {2078825},
 publisher = {Society for Industrial and Applied Mathematics},
 address = {Philadelphia, PA},
 keywords = {algebraic multigrid, interpolation, non-Hermitian, nonsymmetric, smoothed aggregation},
}

@article{Dorit2011,
author    = {Dorit Ron and
             Ilya Safro and
             Achi Brandt},
title     = {Relaxation-Based Coarsening and Multiscale Graph Organization},
journal   = {Multiscale Modeling {\&} Simulation},
volume    = {9},
number    = {1},
year      = {2011},
pages     = {407-423},
ee        = {http://dx.doi.org/10.1137/100791142}
}
@article{chen2011algebraic,
  title={Algebraic distance on graphs},
  author={Chen, Jie and Safro, Ilya},
  journal={SIAM Journal on Scientific Computing},
  volume={33},
  number={6},
  pages={3468--3490},
  year={2011},
  publisher={SIAM}
}
@inproceedings{Adams04,
	Author = {Adams, M.~F. and Bayraktar, H.~H. and Keaveny, T.~M. and Papadopoulos, P.},
	Booktitle = {ACM/IEEE Proceedings of SC2004: High Performance Networking and Computing},
	Title = {Ultrascalable implicit finite element analyses in solid mechanics with over a half a billion degrees of freedom},
	Note = {Gordon Bell Award},
	Year = {2004}
}

@article{Adams03a,
	Author = {Adams, M.~F.},
	Journal = {Numerical Linear Algebra with Applications},
	Number = {2-3},
	Pages = {141-153},
	Title = {Algebraic multigrid methods for constrained linear systems with applications to contact problems in solid mechanics},
	Volume = {11},
	Year = {2004}
}

@article{Adams-10a,
	Author = {M. ~F. Adams and Ravi Samtaney and Achi Brandt},
	Doi = {DOI: 10.1016/j.jcp.2010.04.024},
	Issn = {0021-9991},
	Journal = {Journal of Computational Physics},
	Keywords = {Implicit magnetohydrodynamics},
	Number = {18},
	Pages = {6208 - 6219},
	Title = {Toward textbook multigrid efficiency for fully implicit resistive magnetohydrodynamics},
	Url = {http://www.sciencedirect.com/science/article/B6WHY-4YY8N52-2/2/4a06d49560a7f24a4da5bb25d0c75d62},
	Volume = {229},
	Year = {2010},
	Bdsk-Url-1 = {http://www.sciencedirect.com/science/article/B6WHY-4YY8N52-2/2/4a06d49560a7f24a4da5bb25d0c75d62},
	Bdsk-Url-2 = {http://dx.doi.org/10.1016/j.jcp.2010.04.024}
}

@inproceedings{Adams98,
	Address = {Copper Mountain, CO},
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	Year = 1998
}

@inproceedings{MadayPatera89,
  author    = {Y. Maday and A. T. Patera},
  title     = {Spectral element methods for the {Navier-Stokes} equations},
  editor    = {A. K. Noor and J. T. Oden},
  booktitle = {State-of-the-Art Surveys in Computational Mechanics},
  pages     = {71-–143},
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  year      = {1989}
}
@article{mishra2012mlmcfvm,
title = "Multi-level {M}onte {C}arlo finite volume methods for nonlinear systems of conservation laws in multi-dimensions",
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volume = 231,
number = 8,
pages = "3365--3388",
year = 2012,
issn = "0021-9991",
doi = "10.1016/j.jcp.2012.01.011",
author = "S. Mishra and Ch. Schwab and J. {\v S}ukys",
keywords = {Conservation laws, Euler, MHD, Uncertainty quantification, Multi-level Monte Carlo, Parallelization}
}
@article{barth2011mlmcfe,
   author = {Barth, Andrea and Schwab, Christoph and Zollinger, Nathaniel},
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   title = {Multi-Level {M}onte {C}arlo Finite Element method for elliptic {PDE}s with stochastic coefficients},
   journal = {Numerische Mathematik},
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   keyword = {Mathematics and Statistics},
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   year = {2011}
}
@article{nguyen2011hybridizable,
  title={Hybridizable discontinuous {G}alerkin methods},
  author={Nguyen, N.C. and Peraire, J. and Cockburn, B.},
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  year={2011},
  publisher={Springer}
}

@Misc{snyder-scidac3:proposal,
  author = {Philip {Snyder (PI)}},
  title  = {{Plasma Edge Advanced Computation (PEAC) Center}},
  note   = {proposal to DOE SciDAC3},
  month = {Oct},
  year = 2011
}

@Misc{wirth-scidac3:proposal,
  author = {Brian {Wirth (PI)}},
  title  = {{Plasma Surface Interactions: Bridging from the Surface to the Micron Frontier through Leadership Class Computing}},
  note   = {proposal to DOE SciDAC3},
  month = {Oct},
  year = 2011
}

@Misc{cary-scidac3:proposal,
  author = {John {Cary (PI)}},
  title  = {{Integrated Multiscale Modeling for Plasma Analysis and Control of Tokamak Stability (IMMPACTS)}},
  note   = {proposal to DOE SciDAC3},
  month = {Oct},
  year = 2011
}

@Misc{vashista-scidac3:proposal,
  author = {Priya {Vashista (PI)}},
  title  = {{Design of Damage-Tolerance Material Interfaces for Extreme Stress-Temperature-Corrosion Environments: Algorithms and Methods for Multi-Petaflops Simulations}},
  note   = {proposal to DOE SciDAC3},
  month = {March},
  year = 2012
}

@Article{Elemental2012,
  author  = {Jack Poulson and Bryan Marker and Jeff R. Hammond and Nichols A. Romero and Robert {v}an~{d}e~{G}eijn},
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  volume  = {39},
  number  = {2},
  year    = {2013}
}

@misc{elemental-web-page,
  author = {Jack Poulson},
  title  = {Elemental: Distributed memory dense linear algebra},
  howpublished = {\url{http://libelemental.org}},
  url    = {http://libelemental.org/},
  year   = {2015}
}

@book{ScalesReport,
  title     = {A Science-based Case for Large-scale Simulation},
  editor    = {D. E. Keyes},
  publisher = {U.S. Department of Energy},
  year      = {2004},
  url       = {http://www.pnl.gov/scales}
}

@InProceedings{Cilk95,
address	= {Santa Barbara, California},
author	= {Robert D. Blumofe and Christopher F. Joerg and Bradley C. Kuszmaul and Charles E. Leiserson and Keith H. Randall and Yuli Zhou},
booktitle	= {Proceedings of the Fifth ACM SIGPLAN Symposium on Principles and Practice of Parallel Programming (PPoPP)},
day	 = {19--21},
month	 = jul,
pages	 = {207--216},
title	 = {{Cilk}: An Efficient Multithreaded Runtime System},
year	 = {1995}
}

@misc{valgrind-web-page,
  author = {Julian Seward},
  title  = {Valgrind},
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  howpublished = {\url{http://valgrind.org/}},
  year   = {2012}
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@article{BLAS79,
  author  = {C.~L. Lawson and R.~J. Hanson and D. Kincaid and F.~T. Krogh},
  title   = {Basic linear algebra subprograms for Fortran usage},
  journal = {ACM Transactions on Mathematical Software},
  volume  = {5},
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  year    = {1979}
}

@techreport{LAPACK90,
  author      = {E. Anderson and Z. Bai and C. Bischof and J. Demmel and J. Dongarra and J. Du~Croz and A. Greenbaum and S. Hammarling and A. McKenney and D. Sorensen},
  title       = {{LAPACK}: A portable linear algebra library for high-performance computers},
  institution = {Computer Science Dept., University of Tennessee},
  number      = {CS-90-105},
  month       = {May},
  year        = {1990}
}

@techreport{NvidiaFermi,
  author      = {NVIDIA},
  title       = {{NVIDIA}'s Next Generation {CUDA} Compute Architecture: {F}ermi},
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  year        = {2009}
}

@misc{IntelMIC,
  author       = {Many Core Group, Cambridge University},
  title        = {Intel Many Integrated Core Architecture},
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  month        = {December},
  year         = {2010}
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@article{AbuSufahKuckLawrie81,
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@inproceedings{GuoBikshandiFraguelaGarzaranPadua08,
 author = {Guo, Jia and Bikshandi, Ganesh and Fraguela, Basilio B. and Garzaran, Maria J. and Padua, David},
 title = {Programming with tiles},
 booktitle = {Proceedings of the 13th ACM SIGPLAN Symposium on Principles and practice of parallel programming},
 series = {PPoPP '08},
 year = {2008},
 isbn = {978-1-59593-795-7},
 location = {Salt Lake City, UT},
 pages = {111--122},
 numpages = {12},
 url = {http://doi.acm.org/10.1145/1345206.1345225},
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 acmid = {1345225},
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}

@article{Strout04,
    Journal = {International Journal of High Performance Computing Applications},
    Year = {2004},
    Title = {Sparse Tiling for Stationary Iterative Methods},
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    Pages = {95-114},
    Volume = {18},
    Number = {1},
    Author = {Michelle Mills Strout and Larry Carter and Jeanne Ferrante and Barbara Kreaseck}
}

@misc{OpenCLStandard,
   author       = {Khronos Group},
   title        = {{OpenCL} 1.2 Specification},
   howpublished = {\url{http://www.khronos.org/registry/cl/specs/opencl-1.2.pdf}},
   url          = {http://www.khronos.org/registry/cl/specs/opencl-1.2.pdf},
   year         = {2011}
}

@misc{STLGuide,
   author       = {SGI},
   title        = {Standard Template Library Programmer's Guide},
   howpublished = {\url{http://www.sgi.com/tech/stl/}},
   url          = {http://www.sgi.com/tech/stl/},
   year         = {2011}
}

@book{Stepanov09,
  author    = {Alexander Stepanov and Paul McJones},
  title     = {Elements of Programming},
  publisher = {Addison-Wesley},
  isbn      = {978-0-321-63537-2},
  year      = {2009}
}

@Article{BangerthHartmannKanschat2007,
	  author = 	 {W. Bangerth and R. Hartmann and G. Kanschat},
	  title = 	 {{deal.II} -- a General Purpose Object Oriented Finite Element Library},
	  journal = 	 {ACM Trans. Math. Softw.},
	  year = 	 2007,
	  volume = 	 33,
	  number = 	 4,
	  pages = 	 {24/1--24/27}
}

@misc{dealii-web-page,
   author       = {W. Bangerth and R. Hartmann and G. Kanschat},
   title        = {{deal.II}},
   howpublished = {\url{http://www.dealii.org/}},
   url          = {http://www.dealii.org/},
   year         = {2012}
}
@Inbook{Siek2012,
  title     = {The C++0x ``Concepts'' Effort},
  author    = {Jeremy G. Siek},
  editor    = {Jeremy Gibbons},
  bookTitle = {Generic and Indexed Programming: International Spring School, SSGIP 2010, Oxford, UK, March 22-26, 2010, Revised Lectures},
  pages     = {175--216},
  isbn      = {978-3-642-32202-0},
  doi       = {10.1007/978-3-642-32202-0_4},
  url       = {http://arxiv.org/abs/1201.0027},
  note      = {\url{http://arxiv.org/abs/1201.0027}},
  publisher = {Springer Berlin Heidelberg},
  year      = {2012},
}

@misc{sharpclaw,
note = {\url{http://numerics.kaust.edu.sa/sharpclaw}},
author = {Ketcheson, D. I. and Parsani, M.},
keywords = {clawpack,finite volumes,godunov type methods,high order methods,hyperbolic PDEs,sharpclaw,software},
mendeley-tags = {clawpack,finite volumes,godunov type methods,high order methods,hyperbolic PDEs,sharpclaw,software},
title = {{SharpClaw software}},
year = {2011}
}

@book{Leveque2002,
  title  = {Finite volume methods for hyperbolic problems},
  author = {Randall J LeVeque},
  volume = {31},
  year   = {2002},
}
@misc{clawpack45,
note = {\url{http://www.clawpack.org}},
author = {LeVeque, R. J. and Berger, M. J.},
keywords = {clawpack,finite volumes,hyperbolic PDEs,software},
mendeley-tags = {clawpack,finite volumes,hyperbolic PDEs,software},
title = {{Clawpack Software version 4.5}},
url = {www.clawpack.org},
year = {2011}
}

@article{Nilsen2010,
archivePrefix = {arXiv},
arxivId = {arXiv:1002.0705v1},
author = {Nilsen, J.K. and Cai, X. and H{\o}yland, Bj{\o} rn and Langtangen, H. P.},
eprint = {arXiv:1002.0705v1},
file = {:Users/ketch/Documents/Mendeley Desktop/Nilsen et al/2010 - Simplifying the parallelization of scientific codes by a function-centric approach in Python.pdf:pdf},
journal = {Computational Science \& Discovery},
keywords = {parallel,programming,python,software},
mendeley-tags = {parallel,programming,python,software},
pages = {015003},
publisher = {IOP Publishing},
title = {{Simplifying the parallelization of scientific codes by a function-centric approach in Python}},
url = {http://iopscience.iop.org/1749-4699/3/1/015003},
volume = {3},
year = {2010}
}

@book{Langtangen09,
  author    = {Hans Petter Langtangen},
  title     = {Python Scripting for Computational Science},
  publisher = {Springer},
  series    = {Texts in Computational Science and Engineering},
  pages     = {784},
  isbn      = {3540739157},
  year      = {2009}
}

@book{NumpyGuide,
  author    = {Travis E. Oliphant},
  title     = {Guide to Numpy},
  publisher = {Trelgol},
  year      = {2008}
}

@misc{PyCUDA,
   author       = {Andreas Kl\"ockner},
   title        = {{PyCUDA}},
   howpublished = {\url{http://mathema.tician.de/software/pycuda}},
   year         = {2011}
}

@misc{PyOpenCL,
   author       = {Andreas Kl\"ockner},
   title        = {{PyOpenCL}},
   howpublished = {\url{http://mathema.tician.de/software/pyopencl}},
   year         = {2011}
}
@article{Klockner2012,
  author  = {Andreas Kl\"{o}ckner and Nicolas Pinto and Yunsup Lee and Bryan Catanzaro and Paul Ivanov and Ahmed Fasih},
  title   = {{PyCUDA} and {PyOpenCL}: A scripting-based approach to {GPU} run-time code generation},
  journal = {Parallel Computing},
  volume  = {38},
  number  = {3},
  pages   = {157--174},
  year    = {2012},
  issn    = {0167-8191},
  doi     = {10.1016/j.parco.2011.09.001},
  url     = {http://www.sciencedirect.com/science/article/pii/S0167819111001281}
}

%%%%%% Matt Stuff %%%%%%
@misc{knepley:icerm-workshop:2012,
 author = {David Keyes and Matthew Knepley and Katherine Yelick},
 title  = {Synchronization-reducing and Communication-reducing Algorithms and Programming Models for Large-scale Simulations},
 note   = {Workshop sponsored by the Institute for Computational and Experimental Research in Mathematics (ICERM), Jan. 9-13, 2012, Providence, RI, \url{http://icerm.brown.edu/tw12-1-exascale}},
 year   = {2012}
}

@techreport{KirbyKnepleyScott04,
  author      = {Robert C. Kirby and Matthew G. Knepley and L. Ridgway Scott},
  title       = {Optimal Evaluation of Finite Element Matrices},
  type        = {Technical Report},
  number      = {TR-2004-04},
  institution = {University of Chicago},
  url         = {http://www.cs.uchicago.edu/research/publications/techreports/TR-2004-04},
  note        = {\url{http://www.cs.uchicago.edu/research/publications/techreports/TR-2004-04}},
  pages       = {14},
  month       = {May},
  year        = {2004}
}

@techreport{KirbyKnepleyScott10,
  author      = {Robert C. Kirby and Matthew G. Knepley and L. Ridgway Scott},
  title       = {Languages and Compilers for Variational Forms},
  type        = {Technical Report},
  number      = {TR-2010-09},
  institution = {University of Chicago},
  url         = {http://www.cs.uchicago.edu/research/publications/techreports/TR-2010-09},
  note        = {\url{http://www.cs.uchicago.edu/research/publications/techreports/TR-2010-09}},
  month       = {October},
  year        = {2010}
}

@techreport{KirbyKnepleyScott10b,
  author      = {Robert C. Kirby and Matthew G. Knepley and L. Ridgway Scott},
  title       = {Evaluation of the Action of Finite Element Operators},
  type        = {Technical Report},
  number      = {TR-2010-08},
  institution = {University of Chicago},
  url         = {http://www.cs.uchicago.edu/research/publications/techreports/TR-2010-08},
  note        = {\url{http://www.cs.uchicago.edu/research/publications/techreports/TR-2010-08}},
  month       = {October},
  year        = {2010}
}

@techreport{BruneKnepleyScott11,
  author      = {Peter R. Brune and Matthew G. Knepley and L. Ridgway Scott},
  title       = {Exponential grids in high-dimensional space},
  type        = {Technical Report},
  number      = {TR-2011-07},
  institution = {University of Chicago},
  url         = {http://www.cs.uchicago.edu/research/publications/techreports/TR-2011-07},
  note        = {\url{http://www.cs.uchicago.edu/research/publications/techreports/TR-2011-07}},
  month       = {December},
  year        = {2011}
}

@techreport{Zheng11,
  author      = {Liang Zheng and Taras Gerya and Matthew G. Knepley and David A. Yuen and Huai Zhang and Yaolin Shi},
  title       = {Implementation of a multigrid solver on {GPU} for {Stokes} equations with strongly variable viscosity based on {Matlab} and {CUDA}},
  type        = {Research Report},
  number      = {UMSI 2011/33},
  institution = {University of Minnesota Supercomputing Institute},
  url         = {http://static.msi.umn.edu/rreports/2011/33.pdf},
  note        = {\url{http://static.msi.umn.edu/rreports/2011/33.pdf}},
  month       = {March},
  year        = {2011}
}

@inproceedings{Zheng2010,
  author       = {Liang Zheng and Taras Gerya and David A. Yuen and Matthew G. Knepley and Huai Zhang and Yaolin Shi},
  title        = {{GPU} Implementation of {Stokes} Equation with Strongly Variable Coefficients},
  booktitle    = {Eos Transactions of the AGU},
  organization = {American Geophysical Union},
  note         = {Fall Meeting Supplemental, Abstract IN41A-1350},
  year         = {2010}
}

@incollection{TerrelKirbyKnepleyScott12,
  author    = {Andy R. Terrel and Robert C. Kirby and Matthew G. Knepley and L. Ridgway Scott and Garth N. Wells},
  title     = {Finite elements for incompressible fluids},
  editors   = {A. Logg and K.A. Mardal and G. N. Wells},
  booktitle = {Automated solutions of differential equations by the finite element method},
  series    = {Lecture Notes in Computational Science and Engineering},
  volume    = {84},
  pages     = {163--169},
  publisher = {Springer-Verlag},
  year      = {2012}
}

@incollection{KirbyKnepleyLoggScottTerrel12,
  author    = {Robert C. Kirby and Matthew G. Knepley and Anders Logg and L. Ridgway Scott and Andy R. Terrel},
  title     = {Discrete optimization of finite element matrix evaluation},
  editors   = {A. Logg and K.A. Mardal and G. N. Wells},
  booktitle = {Automated solutions of differential equations by the finite element method},
  series    = {Lecture Notes in Computational Science and Engineering},
  volume    = {84},
  pages     = {385--397},
  publisher = {Springer-Verlag},
  year      = {2012}
}
@incollection{Kirby12,
  author    = {Robert C. Kirby},
  title     = {{FIAT}: Numerical Construction of Finite Element Basis Functions},
  editors   = {A. Logg and K.A. Mardal and G. N. Wells},
  booktitle = {Automated solutions of differential equations by the finite element method},
  series    = {Lecture Notes in Computational Science and Engineering},
  volume    = {84},
  publisher = {Springer-Verlag},
  year      = {2012}
}
@article{BrownConveryHotesKnepleyPetropolous1993,
  author  = {Robert W. Brown and Mary Convery and Scott Hotes and Matthew G. Knepley and Labros Petropolous},
  title   = {Closed strings with low harmonics and kinks},
  journal = {Physical Review D},
  volume  = {48},
  number  = {6},
  year    = {1993}
}

@article{Minimax1996,
  title   = {MiniMax: What has been learned thus far},
  author  = {Mary E. Convery and W.~L. Davis and Ken W. Del Signore and Tom L. Jenkins and Erik Kangas and Matthew G. Knepley and Ken L. Kowalski and Cyrus C. Taylor and C.~H. Wang and S.~H. Oh and W.~D. Walker and P.~L. Colestock and B. Hanna and M. Martens and J. Streets and R.~C. Ball and H.~R. Gustafson and L.~W. Jones and M.~J. Longo and J.~D. Bjorken and N. Morgan and C.~A. Pruneau},
  journal = {Nuovo Cimento},
  volume  = {19},
  number  = {1},
  pages   = {1045--1049},
  year    = {1996}
}

@article{Minimax1997,
  author  = {Minimax Collaboration},
  title   = {Analysis of Charged Particle/Photon Correlations in Hadronic Multiparticle Production},
  journal = {Physical Review D},
  volume  = {55},
  number  = {9},
  year    = {1997}
}

@article{Minimax2000,
  author  = {Minimax Collaboration},
  title   = {Search for disoriented chiral condensate at the {Fermilab} {Tevatron}},
  journal = {Physical Review D},
  volume  = {61},
  number  = {3},
  year    = {2000}
}

@article{KirbyKnepleyLoggScott05,
  author  = {Robert C. Kirby and Matthew G. Knepley and Anders Logg and L. Ridgway Scott},
  title   = {Optimizing the evaluation of finite element matrices},
  journal = {SIAM Journal on Scientific Computing},
  volume  = {27},
  number  = {3},
  pages   = {741--758},
  year    = {2005}
}

@article{BardhanKnepleyAnitescu2008,
  author  = {Jaydeep P. Bardhan and Matthew G. Knepley and Mihai Anitescu},
  title   = {Bounding the Electrostatic Free Energies Associated with Linear Continuum Models of Molecular Solvation},
  journal = {Journal of Chemical Physics},
  volume  = {130},
  number  = {10},
  pages   = {104108},
  note    = {Selected for the March 15, 2009 issue of Virtual Journal of Biological Physics Research, \url{http://dx.doi.org/10.1063/1.3081148}},
  year    = {2008}
}

%Poster at Biophysical Society Fall Meeting
@article{BardhanKnepley2017,
  author       = {Jaydeep P. Bardhan and Matthew G. Knepley},
  title        = {Accurate Atom-by-Atom Predictions of Solvation Electrostatics Using a Hydration-Shell {Poisson}-{Boltzmann} Model},
  journal      = {Biophysical Journal},
  volume       = {110},
  number       = {3},
  note         = {Fall Meeting Supplemental, Abstract DI14A-08},
  doi          = {10.1016/j.bpj.2015.11.1766},
  year         = {2017}
}

@article{TabriziRahimiGoossensKnepleyBardhan2018,
  title   = {Solvation Thermodynamics of Neutral and Charged Solutes Using the Solvation-Layer Interface Condition (SLIC) Continuum Dielectric Model},
  author  = {Amirhossein Molavi Tabrizi and Ali Mehdizadeh Rahimi and Spencer Goossens and Matthew G. Knepley and Jaydeep P. Bardhan},
  journal = {International Journal of Quantum Chemistry},
  note    = {Accepted},
  year    = {2018}
}

@article{Knepley2010,
  author  = {Stodden, V. and Knepley, M. G. and Wiggins, C. and LeVeque, R. J. and Donoho, D. and Fomel, S. and Friedlander, M. P. and Gerstein, M. and Mitchell, I. and Ouellette, L. L. and Bramble, N. W. and Brown, P. O. and Carey, V. and DeNardis, L. and Gentleman, R. and {Gezelter, J}, D. and Goodman, A. and Moore, J. E. and Pasquale, F. A. and Rolnick, J. and Seringhaus, M. and Subramanian, R.},
  title   = {{Reproducible Research: addressing the need for data and code sharing in computational science}},
  journal = {Computing in Science and Engineering},
  volume  = {12},
  number  = {5},
  pages   = {8--13},
  url     = {http://www.bepress.com/cgi/viewcontent.cgi?article=1034\&amp;amp;context=sagmb},
  year    = {2010}
}

@article{KetchesonAhmadiaKnepley2011,
  title   = {Conference Review: High Performance Computing and Hybrid Programming Concepts for Hyperbolic PDE Codes},
  author  = {David I. Ketcheson and Aron Ahmadia and Matthew G. Knepley},
  journal = {SIAM News},
  volume  = {44},
  number  = {7},
  month   = {September},
  note    = {\url{http://www.siam.org/pdf/news/1912.pdf}},
  year    = {2011}
}

@article{YokotaBardhanKnepleyBarbaHamada2011,
  author  = {Rio Yokota and Jaydeep P. Bardhan and Matthew G. Knepley and L.A. Barba and Tsuyoshi Hamada},
  title   = {Biomolecular electrostatics using a fast multipole {BEM} on up to 512 {GPU}s and a billion unknowns},
  journal = {Computer Physics Communications},
  volume  = {182},
  number  = {6},
  pages   = {1272--1283},
  year    = {2011},
  issn    = {0010-4655},
  doi     = {10.1016/j.cpc.2011.02.013},
  note    = {\url{http://arxiv.org/abs/1007.4591}},
  url     = {http://www.sciencedirect.com/science/article/pii/S0010465511000750}
}

@article{BardhanKnepley2011,
  author  = {Jaydeep P. Bardhan and Matthew G. Knepley},
  title   = {Mathematical Analysis of the {BIBEE} Approximation for Molecular Solvation: Exact Results for Spherical Inclusions},
  journal = {Journal of Chemical Physics},
  volume  = {135},
  number  = {12},
  pages   = {124107--124117},
  url     = {http://arxiv.org/abs/1109.0651},
  note    = {\url{http://arxiv.org/abs/1109.0651}},
  year    = {2011}
}

@article{BruneKnepleyScott2013,
  author  = {Peter R. Brune and Matthew G. Knepley and L. Ridgway Scott},
  title   = {Unstructured Geometric Multigrid in Two and Three Dimensions on Complex and Graded Meshes},
  journal = {SIAM Journal on Scientific Computing},
  url     = {http://arxiv.org/abs/1104.0261},
  note    = {\url{http://arxiv.org/abs/1104.0261}},
  volume  = {35},
  number  = {1},
  pages   = {A173--A191},
  year    = {2013}
}

@article{BardhanKnepley2012a,
  author  = {Jaydeep P. Bardhan and Matthew G. Knepley},
  title   = {Computational science and re-discovery: open-source implementations of ellipsoidal harmonics for problems in potential theory},
  journal = {Computational Science \& Discovery},
  volume  = {5},
  pages   = {014006},
  url     = {http://iopscience.iop.org/1749-4699/5/1/014006/},
  note    = {\url{http://arxiv.org/abs/1204.0267}},
  doi     = {doi:10.1088/1749-4699/5/1/014006},
  year    = {2012}
}

@article{KreienkampEtAl2013,
  author  = {Amy Kreienkamp and Lucy Y. Liu and Mona S. Minkara and Matthew G. Knepley and Jaydeep P. Bardhan and Mala L. Radhakrishnan},
  title   = {Analysis of fast boundary-integral approximations for modeling electrostatic contributions of molecular binding},
  journal = {Molecular Based Mathematical Biology},
  volume  = {1},
  pages   = {124--150},
  doi     = {10.2478/mlbmb-2013-0007},
  issn    = {2299-3266},
  month   = {June},
  note    = {\url{http://www.degruyter.com/view/j/mlbmb.2012.1.issue/mlbmb-2013-0007/mlbmb-2013-0007.xml}},
  year    = {2013}
}

@article{BardhanKnepleyBrune2015,
  author  = {Jaydeep P. Bardhan and Matthew G. Knepley and Peter R. Brune},
  title   = {Analytical Nonlocal Electrostatics Using Eigenfunction Expansions of Boundary-Integral Operators},
  journal = {Molecular Based Mathematical Biology},
  volume  = {3},
  number  = {1},
  pages   = {1--22},
  doi     = {10.1515/mlbmb-2015-0001},
  url     = {http://dx.doi.org/10.1515/mlbmb-2015-0001},
  note    = {\url{http://dx.doi.org/10.1515/mlbmb-2015-0001}},
  year    = {2015}
}

@article{BardhanKnepley14,
  author  = {Jaydeep P. Bardhan and Matthew G. Knepley},
  title   = {Modeling Charge-Sign Asymmetric Solvation Free Energies With Nonlinear Boundary Conditions},
  journal = {Journal of Chemical Physics},
  volume  = {141},
  number  = {13},
  pages   = {131103},
  url     = {http://scitation.aip.org/content/aip/journal/jcp/141/13/10.1063/1.4897324},
  note    = {\url{http://dx.doi.org/10.1063/1.4897324}},
  year    = {2014}
}

@inproceedings{BardhanTejaniWieckowskiRamaswamyKnepley2015,
  title     = {A Nonlinear Boundary Condition for Continuum Models of Biomolecular Electrostatics},
  author    = {Jaydeep P. Bardhan and D. A. Tejani and N. S. Wieckowski and A. Ramaswamy and Matthew G. Knepley},
  booktitle = {Proceedings of PIERS},
  pages     = {1215--1221},
  month     = {July},
  url       = {http://piers.org/piersproceedings/piers2015PragueProc.php?start=250},
  year      = {2015}
}

@article{TabriziKnepleyBardhan2016,
  title   = {Generalising the mean spherical approximation as a multiscale, nonlinear boundary condition at the solute-solvent interface},
  author  = {Amirhossein Molavi Tabrizi and Matthew G. Knepley and Jaydeep P. Bardhan},
  journal = {Molecular Physics},
  volume  = {114},
  number  = {16-17},
  pages   = {2558--2567},
  doi     = {10.1080/00268976.2016.1198503},
  url     = {http://www.tandfonline.com/doi/full/10.1080/00268976.2016.1198503},
  year    = {2016}
}

% http://tex.stackexchange.com/questions/155532/biblatex-and-pubmed-pubmed-central-ids
@article{TabriziGoossensRahimiKnepleyBardhan2017,
  title   = {Predicting Solvation Free Energies and Thermodynamics in Polar Solvents and Mixtures Using a Solvation-Layer Interface Condition},
  author  = {Amirhossein Molavi Tabrizi and Spencer Goossens and Ali Mehdizadeh Rahimi and Matthew G. Knepley and Jaydeep P. Bardhan},
  journal = {Journal of Chemical Physics},
  volume  = {146},
  number  = {9},
  pages   = {094103},
  url     = {http://scitation.aip.org/content/aip/journal/jcp/146/9/10.1063/1.4977037},
  eprint  = {https://arxiv.org/abs/1611.02150},
  doi     = {10.1063/1.4977037},
  note    = {PMCID: PMC5336475},
  year    = {2017}
}

@article{TabriziGoossensCooperKnepleyBardhan2017,
  title   = {Extending the Solvation-Layer Interface Condition {(SLIC)} Continum Electrostatic Model to Linearized {Poisson}-{Boltzmann} Solvent},
  author  = {Amirhossein Molavi Tabrizi and Spencer Goossens and Christopher D. Cooper and Matthew G. Knepley and Jaydeep P. Bardhan},
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  year    = {2017}
}

@inproceedings{McClanahan2011,
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 author = {Wolfgang Bangerth and Carsten Burstedde and Timo Heister and Martin Kronbichler},
 title = {Algorithms and Data Structures for Massively Parallel Generic Adaptive Finite Element Codes},
 journal = {ACM Trans. Math. Softw.},
 issue_date = {December 2011},
 volume = {38},
 number = {2},
 month = jan,
 year = {2012},
 issn = {0098-3500},
 pages = {14:1--14:28},
 articleno = {14},
 numpages = {28},
 url = {http://doi.acm.org/10.1145/2049673.2049678},
 doi = {10.1145/2049673.2049678},
 acmid = {2049678},
 publisher = {ACM},
 address = {New York, NY, USA},
 keywords = {Adaptive mesh refinement, object-orientation, parallel algorithms, software design},
}
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@article{CaiLi2011,
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@article{Cai2009,
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@techreport{gropp1993sowing2,
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@techreport{gropp1993simplified,
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@misc{SimplifiedBSD,
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@book{ChaconStraub14,
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@misc{Bitbucket,
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@misc{GitWorkflows,
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@misc{FigShare,
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@inproceedings{beazley1996swig,
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@misc{SoftwareProductivityWorkshopReport14,
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@misc{SoftwareProductivityWhitepaper13,
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@Misc{IDEAS:project,
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@Misc{ sawsFS-web-page,
  author =       "Surtai Han and Barry Smith and Hong Zhang",
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@Misc{ sawsHK-web-page,
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@Misc{ sawsNestK-web-page,
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}

@misc{m2acs:project,
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@misc{hssmn13,
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  year = 2013
}

@misc{atpesc:website,
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@article{SimonGogotsi08,
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@article{VladSinghRollandMelinteAjayanGohy14,
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@article{LiChengShashurinKeidar12,
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  year    = {2012},
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@article{Miller07,
  title   = {A Brief History of Supercapacitors},
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}
@book{Deshpande14,
  title     = {Ultracapacitors: Future of Energy Storage},
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@article{HoJowBoggs10,
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@article{Gillespie14,
  title   = {A review of steric interactions of ions: Why some theories succeed and others fail to acount for ion size},
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@article{GillespieValiskoBoda05,
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  year    = {2005}
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@article{ValiskoBodaGillespie07,
  author  = {Monica Valisk\'{o} and Dezs\H{o} Boda and Dirk Gillespie},
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@article{Gillespie08,
  author  = {Dirk Gillespie},
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  year    = {2008}
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@article{LiWuWang15,
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}
@article{Gillespie12,
  title   = {High energy conversion efficiency in nanofluidic channels},
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}
@article{Dieterich79,
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@article{BodaKovacsGillespieKristof14,
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@article{Rosenfeld89,
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@article{SchindlerMitchellMcCabeCummingsLeVan13,
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@misc{TRAMONTO,
  author = {Laura Frink and et. al.},
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@incollection{ZhongYuenMoresiKnepley15,
  author    = {Shijie Zhong and David A. Yuen and Louis N. Moresi and Matthew G. Knepley},
  title     = {Numerical Methods for Mantle Convection},
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  publisher = {Elsevier},
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  editor    = {Gerald Schubert},
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  year      = {2015},
}
@article{Richarson1911,
  author    = {Lewis Fry Richardson},
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  number    = {459--470},
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@article{Kirkwood34,
  author  = {John G. Kirkwood},
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@techreport{schoof1994exodus,
  title   = {{EXODUS II}: a finite element data model},
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@misc{poirier1998cgns,
  author  = {Diane Poirier and Steven R Allmaras and Douglas R McCarthy and Matthew F Smith and Fancis Y Enomoto},
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  year    = {1998}
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@article{geuzaine2009gmsh,
  title   = {Gmsh: A 3-D finite element mesh generator with built-in pre-and post-processing facilities},
  author  = {Christophe Geuzaine and Jean-Fran{\c{c}}ois Remacle},
  journal = {International Journal for Numerical Methods in Engineering},
  volume  = {79},
  number  = {11},
  pages   = {1309--1331},
  year    = {2009},
  publisher = {Wiley Online Library}
}

@article{Si2015,
  title   = {{TetGen}, a {Delaunay}-Based Quality Tetrahedral Mesh Generator},
  author  = {Hang Si},
  journal = {ACM Trans. on Mathematical Software},
  volume  = {41},
  number  = {2},
  month   = {February},
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  year    = {2015},
}

@article{Bjorck1994,
  title   = {Numerics of Gram-Schmidt orthogonalization},
  author  = {{\AA}ke Bj{\"o}rck},
  journal = {Linear Algebra and Its Applications},
  volume  = {197},
  pages   = {297--316},
  year    = {1994},
  publisher = {Elsevier}
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@phdthesis{Yood05,
  author = {Charles Nelson Yood},
  title  = {Argonne National Laboratory and the Emergence of Computer and Computational Science, 1946--1992},
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  month  = {August},
  year   = {2005},
}

@article{FearnleySander79,
  title   = {Hermann Grassmann and the Creation of Linear Algebra},
  author  = {Desmond Fearnley-Sander},
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  volume  = {86},
  pages   = {809--817},
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@incollection{Knepley2012,
  author       = {Matthew G. Knepley},
  title        = {Programming Languages for Scientific Computing},
  booktitle    = {Encyclopedia of Applied and Computational Mathematics},
  publisher    = {Springer},
  year         = 2012,
  editor       = {Bj\"orn Engquist},
  doi          = {10.1007/978-3-540-70529-1},
  url          = {http://arxiv.org/abs/1209.1711},
  note         = {\url{http://arxiv.org/abs/1209.1711}},
}
@Inbook{Knepley2015,
  title     = {Programming Languages for Scientific Computing},
  author    = {Matthew G. Knepley},
  bookTitle = {Encyclopedia of Applied and Computational Mathematics},
  editor    = {Bj{\"o}rn Engquist},
  publisher = {Springer Berlin Heidelberg},
  address   = {Berlin, Heidelberg},
  pages     = {1173--1181},
  isbn      = {978-3-540-70529-1},
  doi       = {10.1007/978-3-540-70529-1_250},
  url       = {https://doi.org/10.1007/978-3-540-70529-1_250},
  year      = {2015}
}

@book{Hughes2000,
  author = {Thomas J. R. Hughes},
  title  = {The Finite Element Method: Linear Static and Dynamic Finite Element Analysis},
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  pages  = {704},
  year   = {2000},
  isbn   = {978-0486411811},
  publisher = {Dover}
}

@article{Roache2002,
  title   = {Code verification by the method of manufactured solutions},
  author  = {Patrick J. Roache},
  journal = {Journal of Fluids Engineering},
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  number  = {1},
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  year    = {2002},
  publisher = {American Society of Mechanical Engineers}
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@incollection{RokosGorman13,
  title     = {PRAgMaTIc - Parallel Anisotropic Adaptive Mesh Toolkit},
  author    = {Georgios Rokos and Gerard Gorman},
  booktitle = {Facing the Multicore-Challenge III},
  series    = {Lecture Notes in Computer Science},
  editor    = {Keller, Rainer and Kramer, David and Weiss, Jan-Philipp},
  publisher = {Springer Berlin Heidelberg},
  volume    = {7686},
  pages     = {143-144},
  doi       = {10.1007/978-3-642-35893-7_22},
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  url       = {http://dx.doi.org/10.1007/978-3-642-35893-7_22},
  year      = {2013},
}

@misc{hdf5:homepage,
   author       = {{The HDF Group}},
   title        = {The {HDF5} Homepage},
   howpublished = {\url{https://www.hdfgroup.org/HDF5/}},
   year         = {2015}
}

@misc{paraview:homepage,
   author       = {Kitware},
   title        = {The {ParaView} Homepage},
   howpublished = {\url{http://www.paraview.org/}},
   year         = {2015}
}

@misc{xdmf:homepage,
   author       = {Kitware},
   title        = {The Extensible Data Model and Format ({XDMF})},
   howpublished = {\url{http://www.xdmf.org/}},
   year         = {2015}
}

@article{CullerKarp1993,
  title   = {LogP: Towards a realistic model of parallel computation},
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  journal = {SIGPLAN Notices},
  volume  = {28},
  number  = {7},
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  year    = {1993},
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@article{AggarwalVitter1988,
  title   = {The input/output complexity of sorting and related problems},
  author  = {Alok Aggarwal and Jeffrey Vitter},
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  volume  = {31},
  number  = {9},
  pages   = {1116--1127},
  year    = {1988},
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@inproceedings{CzechowskiBattaglinoMcClanahanChandramowlishwaranVuduc2011,
  author    = {Kenneth Czechowski and Casey Battaglino and Chris McClanahan and Aparna Chandramowlishwaran and Richard Vuduc},
  title     = {Balance principles for algorithm-architecture co-design},
  booktitle = {Proc.~USENIX Wkshp. Hot Topics in Parallelism (HotPar)},
  month     = {May},
  address   = {Berkeley, CA, USA},
  url       = {http://www.usenix.org/events/hotpar11/tech/final_files/Czechowski.pdf},
  year      = {2011},
}

@article{WilliamsWatermanPatterson2009,
  title   = {Roofline: an insightful visual performance model for multicore architectures},
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  journal = {Communications of the ACM},
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  number  = {4},
  pages   = {65--76},
  year    = {2009},
  publisher = {ACM}
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@misc{roofline-web-page,
  author = {Samuel Williams and {et. al.}},
  title  = {{R}oofline {P}erformance {M}odel},
  key    = "Roofline",
  url    = {http://crd.lbl.gov/departments/computer-science/performance-and-algorithms-research/research/roofline/},
  howpublished = {\url{http://crd.lbl.gov/departments/computer-science/performance-and-algorithms-research/research/roofline/}},
}

@misc{roofline-talk2008,
  author = {Samuel Williams and David Patterson},
  title  = {{R}oofline {P}erformance {M}odel},
  key    = {Roofline},
  year   = {2008},
  note   = {ParLab Summer Retreat},
  url    = {http://crd.lbl.gov/assets/pubs_presos/parlab08-roofline-talk.pdf},
  howpublished = {\url{http://crd.lbl.gov/assets/pubs_presos/parlab08-roofline-talk.pdf}},
}

@article{Lee2006,
  title   = {The problem with threads},
  author  = {Edward A Lee},
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  number  = {5},
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  url     = {http://ptolemy.eecs.berkeley.edu/publications/papers/06/problemwithThreads/},
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@article{Hoefler2012,
  title   = {{Optimization principles for collective neighborhood communications}},
  author  = {Torsten Hoefler and Timo Schneider},
  journal = {International Conference for High Performance Computing, Networking, Storage and Analysis, SC},
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@book{Traub1964,
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@inproceedings{BursteddeGhattasGurnisIsaacStadlerWarburtonWilcox2010,
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@inproceedings{IsaacBursteddeGhattas2012,
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@article{IsaacPetraStadlerGhattas2015,
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@article{IsaacBursteddeWilcoxGhattas2015,
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  note    = {accepted},
  year    = {2015}
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@article{IsaacStadlerGhattas2015,
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@inproceedings{RudiMalossiIsaacStadlerGurnisStaarIneichenBekasCurioniGhattas2015,
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  organization = {ACM}
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@article{BunchHopcroft1974,
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@article{Nemirovsky1991,
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@misc{SIAMCSEPrize,
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@article{Rathgeber2017,
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@article{Kirby2006B,
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@article{Luporini2015,
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@article{Markall2012,
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@article{Markall2010,
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@article{LongKirbyWaanders2010,
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  volume={32},
  number={6},
  pages={3323--3351},
  year={2010},
  publisher={SIAM}
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@article{Kirby2010,
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  number  = {2},
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@article{Kirby2014,
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  number  = {2},
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@article{Kirby2011,
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@article{ArnoldFalkWinther2006,
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@article{ArnoldLogg2014,
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@article{JanssonHoffmanJansson2012,
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@article{RognesHamCotterMcRae2013,
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@article{CotterKirby2014,
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  year    = {2014},
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@article{KirbyKieu2015,
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  volume  = {130},
  number  = {2},
  pages   = {257--291},
  year    = {2015},
  publisher = {Springer}
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@article{BrennanKirby2015,
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  year    = {2015},
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@article{HowleKirbyDillon2013,
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  volume  = {35},
  number  = {5},
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@book{Velic2005,
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@article{VelicKnepleyMay2016,
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@article{SterckWinlaw2015,
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@book{LadevezeSimmonds1999,
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@inproceedings{WalkerWoodwardYang2010,
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@article{LottWalkerWoodwardYang2012,
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@inproceedings{BekasSC15,
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@Misc{SIAM:FellowsProgram,
  title = {{Society for Industrial and Applied Mathematics, Fellows Program}},
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  howpublished = "\url{http://www.siam.org/prizes/fellows}",
}

@Misc{R-and-D100:Awards2009,
  title = {{R\&D100 Award Winners 2009}},
  key = {{R\&D100 Award Winners 2009}},
  howpublished = "\url{https://www.rdmag.com/2009/08/2009-r-d-100-award-winners}"
}

@Misc{xsdk:website,
  title ="{xSDK: Extreme-scale Scientific Software Development Kit}",
  key ="xSDK: Extreme-scale Scientific Software Development Kit",
  howpublished="\url{https://xsdk.info}"
}

@misc{xSDK-community-installation-policies2017,
  title  = {{xSDK} Community Installation Policies: {GNU Autoconf} and {CMake} Options},
  author = {R. Bartlett and J. Sarich and B. Smith and T. Gamblin and {xSDK developers}},
  note   = {version 0.3, November 7, 2017, \url{https://dx.doi.org/10.6084/m9.figshare.4495133}},
  year   = 2017
}

@misc{xSDK-community-package-policies2017,
  title  = {{xSDK} Community Package Policies},
  author = {B. Smith and R. Bartlett and {xSDK developers}},
  note   = {version 0.3, November 7, 2017,
           \url{https://dx.doi.org/10.6084/m9.figshare.4495136}},
  year   = 2017
}

@misc{ideas-what-are-interoperable-libraries,
  title  = {What Are Interoperable Software Libraries: Introducing the {xSDK}},
  author = {Lois Curfman McInnes and Michael A. Heroux and Xiaoye Li and Barry Smith and Ulrike Yang and {all xSDK developers}},
  note   = {IDEAS {\em WhatIs} document, version 0.2, April 25, 2016,
            available via \url{https://ideas-productivity.org/resources/howtos/}},
  year   = 2016
}

@Misc{ideas-productivity:website,
  title ="{IDEAS Scientific Software Productivity Project}",
  key ="IDEAS Scientific Software Productivity Project",
  howpublished="\url{https://ideas-productivity.org}"
}

@misc{ECP:website,
  key = {{U.S. DOE Exascale Computing Project (ECP)}},
  title = {{U.S. DOE Exascale Computing Project (ECP)}},
  note = {\url{https://exascaleproject.org}},
  year = 2018
}

@misc{SIAM-CSE-Jan2018,
  author = {Ulrich R\"{u}de and Karen Willcox and Lois Curfman McInnes and Hans {De Sterck} and
           George Biros and Hans Bungartz and James Corones and Evin Cramer
           and James Crowley and Omar Ghattas and Max Gunzburger and Michael Hanke and
           Robert Harrison and Michael Heroux and Jan Hesthaven and Peter Jimack and
           Chris Johnson and Kirk E. Jordan and David E. Keyes and Rolf Krause and Vipin Kumar and
           Stefan Mayer and Juan Meza and Knut Martin M{\o}rken and J. Tinsley Oden and
           Linda Petzold and Padma Raghavan and Suzanne M. Shontz and Anne Trefethen and
           Peter Turner and Vladimir Voevodin and Barbara Wohlmuth and Carol S. Woodward},
  title = {Research and Education in Computational Science and Engineering},
  note = {available via \url{https://arxiv.org/abs/1610.02608}, to appear in {\em SIAM Review}},
  year = {2018}
}

@misc{DOE-AppliedMathPIMeeting2017,
  author = {Jeff Hittinger and Lois Curfman McInnes and Abani Patra and Nathan Baker and
           Miranda Holmes-Cerfon and Barney Maccabe and Esmong Ng and Pieter Swart and Karen Willcox
           and Steven Lee},
  title = {{Report on the 2017 ASCR Applied Mathematics Principal Investigators Meeting}},
  note = {\url{http://www.orau.gov/ascr-appliedmath-pi2017}},
  year = {2017}
}

@misc{DOE-FusionIntegratedSimulationsWorkshopReport2015,
  author = {P. Bonoli and L. C. {McInnes (Chairs)}},
  title = {{Report on the DOE Workshop on Integrated Simulations for Magnetic Fusion Energy Sciences}},
  note = {available via \url{http://science.energy.gov/~/media/fes/pdf/workshop-reports/2016/ISFusionWorkshopReport_11-12-2015.pdf}},
  year = {2015}
}

@misc{SISC-SpecialIssueIntro,
  title = {Introduction to {SISC} Special section associated with {CSE15} on {'CSE Software'} and {'Big Data in CSE'}},
  author = {H. {De Sterck} and C. Johnson and L.C. McInnes},
  month = {November},
  year = 2016,
  journal = "SIAM J. Sci. Comput.",
  note = {available via \url{http://epubs.siam.org/doi/abs/10.1137/16N974188}}
}

@article{xsdk-foundations2017,
  title = {{xSDK} Foundations: Toward an Extreme-scale Scientific Software Development Kit},
  author = {R. Bartlett and I. Demeshko and T. Gamblin and G. Hammond and M. Heroux and
            J. Johnson and A. Klinvex and X. Li and L.C. McInnes and J.D. Moulton and
            D. Osei-Kuffuor and J. Sarich and B. Smith and J. Willenbring and U.M. Yang},
  journal = {Supercomputing Frontiers and Innovations},
  month = {February},
  year = 2017,
  note = {available via \url{https://arxiv.org/abs/1702.08425}}
}

@misc{deal.II:website,
  title = "{{deal.II}: An open-source finite element library}",
  author = "Wolfgang Bangerth and others",
  howpublished="\url{http://www.dealii.org}",
  year = 2018
}

@misc{fission-gas-scidac:website,
  title = "{Simulation of Fission Gas in Uranium Oxide Nuclear Fuel}",
  author = "A. David {Andersson (PI)}",
  howpublished="SciDAC project, \url{https://collab.cels.anl.gov/display/FissionGasSciDAC2}",
  year = 2018
}

@misc{tokamak-disruption-scidac:project,
  title = "{Tokamak Disruption Simulation}",
  author = "Xianzhu {Tang (PI)}",
  howpublished="SciDAC project",
  year = 2018
}
@inproceedings{duplyakin2018memory,
  title={Evaluating Active Learning with Cost and Memory Awareness},
  author={Duplyakin, Dmitry and Brown, Jed and Calhoun, Donna},
  booktitle={2018 IEEE International Parallel and Distributed Processing Symposium (IPDPS)},
  pages={214--223},
  year={2018},
  organization={IEEE},
  pdf={https://jedbrown.org/files/DuplyakinBrownCalhoun-ActiveLearningCostMemoryAware-2018.pdf}
}
@InProceedings{duplyakin2016active,
    author      = "Dmitry Duplyakin and Jed Brown and Robert Ricci",
    title       = "Active Learning in Performance Analysis",
    booktitle   = "Proceedings of the IEEE Cluster Conference",
    year        = 2016,
    month       = Sep,
    url         = "http://www.flux.utah.edu/paper/duplyakin-cluster16",
    pdf         = {https://jedbrown.org/files/DuplyakinBrownRicci-ActiveLearningPerformanceAnalysis-2016.pdf}
}
@misc{XGC1:website,
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  author = "C. S. Chang and others",
  howpublished="\url{https://epsi.pppl.gov/computing/xgc-1}",
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}

@misc{WDMApp-Bhattacharjee-ECP:website,
  title = "{WDMApp: High-Fidelity Whole Device Modeling of Magnetically Confined Fusion Plasmas}",
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  note = "ECP application project",
  howpublished = "\url{https://www.exascaleproject.org/activity/energy-applications}",
  year = 2018
}

@misc{subsurface-Steefel-ECP:website,
  title = "{Subsurface: Exascale Subsurface Simulator of Coupled Flow, Transport, Reactions, and Mechanics}",
  note = "ECP application project",
  author = "C. Steefel and others",
  howpublished="\url{https://www.exascaleproject.org/activity/earth-space-science-applications}",
  year = 2018
}

@article{Chombo-Crunch:2014,
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@article{CourantFriedrichsLewy1967,
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@ARTICLE{gilbert-lemarechal,
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@book{Tarantola2005,
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@article{RutkaiKristof2010,
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@article{MalqvistPeterseim2014,
  title   = {Localization of elliptic multiscale problems},
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@article{BrandtBrannickKahlLivshits2011,
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@inproceedings{BarralAlauzet2014,
  title     = {Large displacement body-fitted {FSI} simulations using a mesh-connectivity-change moving mesh strategy},
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@inproceedings{BarralAlauzetLoseille2015,
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  booktitle = {53rd AIAA Aerospace Sciences Meeting},
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@article{BarralOlivierAlauzet2017,
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  year    = {2017},
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@article{IbanezBarralKrakosLoseilleMichalPark2017,
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  volume  = {203},
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  year    = {2017}
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@inproceedings{ParkBarralIbanezKamenetskiyKrakosMichalLoseille2018,
  title     = {Unstructured Grid Adaptation and Solver Technology for Turbulent Flows},
  author    = {Michael A Park and Nicolas Barral and Daniel Ibanez and Dmitry S Kamenetskiy and Joshua A Krakos and Todd R Michal and Adrien Loseille},
  booktitle = {2018 AIAA Aerospace Sciences Meeting},
  pages     = {1103},
  year      = {2018}
}
@inproceedings{BarralAngeloudisKramerGormanPiggott2018,
  title     = {An anisotropic mesh adaptation approach for regional tidal energy hydrodynamics modelling},
  author    = {Nicolas Barral and Athanasios Angeloudis and Stephan C Kramer and Gerard J Gorman and Matthew D Piggott},
  booktitle = {EGU General Assembly Conference Abstracts},
  volume    = {20},
  pages     = {19168},
  year      = {2018}
}
@article{Principe2009,
title   = {{Mathematical models for thermally coupled low speed flows}},
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number  = {1-4},
pages   = {93--112},
url     = {http://www.m-hikari.com/atam/atam2009/atam1-4-2009/principeATAM1-4-2009.pdf},
year    = {2009}
}
